export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a; module load system; module load parallel/20180122; module load java; export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/juicer_tools.1.8.9/; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-10-03-NextSeq-run/juicer-L1113-Haloferax_volcanii_Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-10-03-NextSeq-run/juicer-L1113-Haloferax_volcanii_Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/all.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bwa-indexes/Haloferax_volcanii_DS2_uid46845_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Haloferax_volcanii_DS2_uid46845/bwa-indexes/all.fa