#!/bin/bash
#SBATCH --job-name=zJ-01r-1
#SBATCH --output=zJ-01r.1.out
#SBATCH --error=zJ-01r.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf
#SBATCH --cpus-per-task=16
#SBATCH --mem=100000
#SBATCH -C NO_GPU
module load java; java -Xmx40G -jar juicer_tools.jar pre /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/juicer-hifiasm.hic.p_ctg/aligned/merged_nodups.txt /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/juicer-hifiasm.hic.p_ctg/aligned/inter_rerun.hic /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/hifiasm.hic.p_ctg.chrom.sizes