antiSMASH on Biowulf

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.


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 antismash

[user@cn3144 ~]$ antismash --cpus 2 Streptomyces_coelicolor.gbk

[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 antismash
antismash --cpus $SLURM_CPUS_PER_TASK Streptomyces_coelicolor.gbk

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. antismash.swarm). For example:

antismash --cpus $SLURM_CPUS_PER_TASK sample1.gbk
antismash --cpus $SLURM_CPUS_PER_TASK sample2.gbk
antismash --cpus $SLURM_CPUS_PER_TASK sample3.gbk
antismash --cpus $SLURM_CPUS_PER_TASK sample4.gbk

Submit this job using the swarm command.

swarm -f antismash.swarm [-g #] [-t #] --module antismash
-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 antimash Loads the antiSMASH module for each subjob in the swarm