Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

A collection of small and efficient programs for performing some common and uncommon tasks with FASTQ  files.

 

• https://homes.cs.washington.edu/~dcjones/fastq-tools/

 

• Module Name: fastqtools (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 fastqtools
[user@cn3144 ~]$ fastq-unique input.fq > outfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load fastqtools
fastq-unique input.fq > outfile

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] batch.sh

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

cd dir1; fastq-unique input.fq > outfile
cd dir2; fastq-unique input.fq > outfile
cd dir3; fastq-unique input.fq > outfile

Submit this job using the swarm command.

swarm -f job.swarm [-g #]--module fastqtools

where

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