#!/bin/bash
#SBATCH --job-name=zJ-Bn-1
#SBATCH --output=zJ-Bn.1.out
#SBATCH --error=zJ-Bn.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf
#SBATCH --cpus-per-task=16
#SBATCH --mem=100000
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.1.8.9/; scripts/juicer.sh -t 60 -D /oak/stanford/groups/akundaje/marinovg/papers/2021_Bigelowiella_nucleomorph/2021-04-26-final-assembly/juicer-L1330-Bigelowiella_natans_Hi-C_MluCI-all_reads_final_assembly -d /oak/stanford/groups/akundaje/marinovg/papers/2021_Bigelowiella_nucleomorph/2021-04-26-final-assembly/juicer-L1330-Bigelowiella_natans_Hi-C_MluCI-all_reads_final_assembly -p /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1330-Bigelowiella_natans_Hi-C_MluCI/final-post-review/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.FINAL.renamed.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1330-Bigelowiella_natans_Hi-C_MluCI/final-post-review/bwa-indexes/Bigelowiella_natans_CCMP2755_v1.0.20+chrM+chrC+NM.FINAL.renamed.fasta