#!/bin/bash
#SBATCH --job-name=zL1322-1
#SBATCH --output=zL1322.1.out
#SBATCH --error=zL1322.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf
#SBATCH --cpus-per-task=16
#SBATCH --mem=100000
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/ENCODE4/ssDNA/2020-01-10-NextSeq-run/juicer-L1322-Chlamydomonas_reinhardtii_CC125-Hi-C -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/ssDNA/2020-01-10-NextSeq-run/juicer-L1322-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