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.

References:

• antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano Nucleic Acids Research (2011) doi: 10.1093/nar/gkr466
• antiSMASH 6.0: improving cluster detection and comparison capabilities. Kai Blin, Simon Shaw, Alexander M Kloosterman, Zach Charlop-Powers, Gilles P van Weezel, Marnix H Medema, & Tilmann Weber Nucleic Acids Research (2021) doi: 10.1093/nar/gkab335.

• antiSMASH Documentation
• antiSMASH on GitHub

• Module Name: antismash (see the modules page for more information)
• Multithreaded via the -c/--cpus argument.
As of version 6.1, the default is 128 cpus, so make sure to set this parameter to what you have allocated.
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • ANTISMASH_HOME
• Example files in $ANTISMASH_HOME/test
• Reference data in /fdb/antismash/

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 $ANTISMASH_HOME/test/Streptomyces_coelicolor.gbk

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load antismash
antismash --cpus $SLURM_CPUS_PER_TASK $ANTISMASH_HOME/test/Streptomyces_coelicolor.gbk

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] antismash.sh

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