export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a; module load java; export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/juicer_tools.1.8.9/; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-09-16-NextSeq-run/juicer-L1028-Emiliania_huxley_Hi-C -d /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2019/2019-09-16-NextSeq-run/juicer-L1028-Emiliania_huxley_Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Haptophyta/Emiliania_huxleyi_CCMP1516_v1.0/GCA_000372725.1_Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0_genomic.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Haptophyta/Emiliania_huxleyi_CCMP1516_v1.0/bwa-indexes/Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Haptophyta/Emiliania_huxleyi_CCMP1516_v1.0/bwa-indexes/GCA_000372725.1_Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0_genomic.fa