#!/bin/bash
#SBATCH --job-name=zJuFk-1
#SBATCH --output=zJuFk.1.out
#SBATCH --error=zJuFk.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf,wjg
#SBATCH --cpus-per-task=16
#SBATCH --mem=100000
#SBATCH -C NO_GPU
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/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-scaffold.FINAL-debris-merged -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-scaffold.FINAL-debris-merged -p /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-3D_DNA-r20/Fugacium_kawagutii_V3_genome_scaffold.FINAL.debris-merged.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C-3D_DNA-r20/bwa-indexes/Fugacium_kawagutii_V3_genome_scaffold.FINAL.debris-merged.fa