HTSeq on Biowulf

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. It is developed by Simon Anders at EMBL Heidelberg.


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 htseq
[user@cn3144 ~]$ htseq-count input.sam input.gff

[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 htseq
htseq-count input.sam input.gff

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. htseq.swarm). For example:

cd dir1; htseq-count input.sam input.gff
cd dir2; htseq-count input.sam input.gff
cd dir3; htseq-count input.sam input.gff
cd dir4; htseq-count input.sam input.gff

Submit this job using the swarm command.

swarm -f htseq.swarm [-t #] --module htseq
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module htseq Loads the htseq module for each subjob in the swarm