Biowulf High Performance Computing at the NIH
seqtk on Biowulf

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.

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$

Batch job
Most jobs should be run as batch jobs.

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

set -e
module load seqtk
seqtk seq -a in.fq.gz > out.fa

Submit this job using the Slurm sbatch command.

sbatch [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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
-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