Biowulf High Performance Computing at the NIH
Exonerate on Biowulf

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.


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 input in bold):

[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 exonerate
[+] Loading exonerate, version 2.2.0...
[user@cn3144 ~]$ exonerate query.fasta target.fasta
[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 exonerate
exonerate query.fasta target.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--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. exonerate.swarm). For example:

exonerate query01.fasta target.fasta
exonerate query02.fasta target.fasta
exonerate query03.fasta target.fasta
exonerate query04.fasta target.fasta

Submit this job using the swarm command.

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