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/2019-12-14-NextSeq-run-2/juicer-L1276-Chlamydomonas_reinhardtii_CC125-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-12-14-NextSeq-run-2/juicer-L1276-Chlamydomonas_reinhardtii_CC125-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/bwa-indexes/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/bwa-indexes/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.fa