Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

• https://github.com/lh3/seqtk

• Module Name: seqtk (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 seqtk
[user@cn3144 ~]$ seqtk seq -a in.fq.gz > out.fa
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load seqtk
seqtk seq -a in.fq.gz > out.fa

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] seqtk.sh

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

cd dir1;seqtk seq -a in.fq.gz > out.fa
cd dir2;seqtk seq -a in.fq.gz > out.fa
cd dir3;seqtk seq -a in.fq.gz > out.fa

Submit this job using the swarm command.

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

where

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