/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-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-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-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-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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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 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-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-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-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-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 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-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-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 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-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-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-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-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-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-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-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-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 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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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 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 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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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 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-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-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-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 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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 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-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