export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.17:$PATH; module load system; module load parallel/20180122; module load java; export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/juicer_tools.2.13.07/; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/10-Acanthamoeba_castellanii/juicer-Acanthamoeba_castellanii_Neff-ASM2102060v1-Hi-C -d /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/10-Acanthamoeba_castellanii/juicer-Acanthamoeba_castellanii_Neff-ASM2102060v1-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Archamoebae/Acanthamoeba_castellanii_Neff-ASM2102060v1/Acanthamoeba_castellanii_Neff-ASM2102060v1.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Archamoebae/Acanthamoeba_castellanii_Neff-ASM2102060v1/bwa-indexes/Acanthamoeba_castellanii_Neff-ASM2102060v1.fa