SRA Toolkit

Example script slurm-sratoolkit.sh to run fastq-dump on 1 node of the cpu partition using 2 cores and at most 4 GB of memory:

slurm-sratoolkit.sh

#!/bin/bash --login
#SBATCH --job-name=sratoolkit
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=4G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --time=0-01:00:00
##SBATCH --account=<account>
 
shopt -q login_shell || exit 1
 
module load sratoolkit
 
fastq-dump --stdout -X $SLURM_CPUS_PER_TASK SRR390728