Antismash

Introduction

Antismash Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

For more information, please check its website: https://biocontainers.pro/tools/antismash and its home page: https://docs.antismash.secondarymetabolites.org.

Versions

• 5.1.2

• 6.0.1

Commands

• antismash

Module

You can load the modules by:

module load biocontainers
module load antismash

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Antismash on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=antismash
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers antismash

antismash --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go --smcog-trees seq.gbk