Purdue University

Commands

• parallel-fastq-dump

Module

You can load the modules by:

module load biocontainers
module load parallel-fastq-dump

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Parallel-fastq-dump on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=parallel-fastq-dump
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers parallel-fastq-dump

parallel-fastq-dump -s SRR11941281/SRR11941281.sra \ 
    --split-files --threads 4 --gzip