#!/bin/bash
#SBATCH --job-name=zFK-3D-1
#SBATCH --output=zFK-3D.1.out
#SBATCH --error=zFK-3D.1.err
#SBATCH --time=160:00:00
#SBATCH -p akundaje,sfgf
#SBATCH --cpus-per-task=1
#SBATCH --mem=100000
#SBATCH -C NO_GPU
./run-asm-pipeline.sh -r 20 --sort-output --build-gapped-map /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Fugacium_kawagutii_V3/bwa-indexes/Fugacium_kawagutii_V3_genome_scaffold.fa /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2023-09-18-Fugacium_kawagutii-Hi-C/juicer-Fugacium_kawagutii_V3-Hi-C/aligned/merged_nodups.txt