#!/bin/bash
#SBATCH --job-name=zJuC2-1
#SBATCH --output=zJuC2.1.out
#SBATCH --error=zJuC2.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf
#SBATCH --cpus-per-task=16
#SBATCH --mem=100000
#SBATCH -C NO_GPU
./run-asm-pipeline.sh -r 20 --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/bowtie-indexes/CDMZ01.fa /oak/stanford/groups/akundaje/marinovg/papers/2026_Chromera_Hi-C/2026-01-16-Ultima-run-Chromera/juicer-L1273+L4897-Chromera_velia-Hi-C/aligned/merged_nodups.txt