#!/bin/bash
#
#SBATCH --job-name=mspiculigera_count    # Nom du jobe
#SBATCH --output=%j.log   # Standard output et error log
#SBATCH --time=2-00:00:00             # Délai max = 7 jours
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=200G
#SBATCH --partition=Lake


cd /scratch/Bio/lmodolo/kmer_diff/

KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
WORK=$(pwd)

# kmdiff count
${KMDIFF} count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 10