Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

FASTA/FASTQ pre-processing programs

• https://github.com/agordon/fastx_toolkit

• Module Name: fastxtoolkit (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load fastxtoolkit
[user@cn3144 ~]$ fastq_to_fasta -i in.fastq -o out.fasta
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. fastxtoolkit.sh). For example:

#!/bin/bash
set -e
module load fastxtoolkit
fastq_to_fasta -i in.fastq -o out.fasta

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] fastxtoolkit.sh

Create a swarmfile (e.g. fastxtoolkit.swarm). For example:

cd dir1; fastq_to_fasta -i in.fastq -o out.fasta
cd dir2; fastq_to_fasta -i in.fastq -o out.fasta
cd dir3; fastq_to_fasta -i in.fastq -o out.fasta

Submit this job using the swarm command.

swarm -f fastxtoolkit.swarm [-g #] --module fastxtoolkit

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module fastxtoolkit	Loads the fastxtoolkit module for each subjob in the swarm