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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

antiSMASH

antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) performs genome-wide identification, annotation and analysis of secondary-metabolite biosynthesis gene clusters in bacterial and fungal genomes.

License

Free to use and open source under GNU AGPLv3.

Available

  • Roihu: 8.0.4, via the bio-apps module.

Usage

antiSMASH is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the antiSMASH module:

module load bio-apps/v202603
module load antismash/8.0.4

Databases

antiSMASH requires reference databases that are not bundled with the module.

Shared reference databases

CSC plans to provide shared reference databases at a central location on Roihu. This is still being set up. Until it is available, download your own copy as shown below.

Download the databases to a writable location (for example your project's /scratch directory) with download-antismash-databases, and point antiSMASH at them with the --databases option:

download-antismash-databases --database-dir /scratch/<project>/antismash_db

Running antiSMASH

antiSMASH takes an annotated genome (GenBank/EMBL) or a FASTA sequence as input. It can use several CPU cores with the --cpus option. Runs should be submitted as batch jobs:

#!/bin/bash
#SBATCH --job-name=antismash
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load antismash/8.0.4

antismash --cpus $SLURM_CPUS_PER_TASK \
    --databases /scratch/<project>/antismash_db \
    --output-dir results \
    genome.gbk

Replace <project> with your CSC project (for example project_2001234), and use the same project in the database path.

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information