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/2020-12-13-NextSeq-run/juicer-L1330-Bigelowiella_natans_Hi-C_MluCI -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-12-13-NextSeq-run/juicer-L1330-Bigelowiella_natans_Hi-C_MluCI -p /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/bwa-indexes/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Chlorarachniophyta/Bigelowiella_natans_CCMP2755_v1.0/bwa-indexes/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.fa