Table of Contents

antismash

The antiSMASH framework allows the detection of clusters of co-occurring biosynthesis genes in genomes, called Biosynthetic Gene Clusters (BGCs). BGCs often contain all the genes required for the biosynthesis of one or more Natural Products (NPs), also known as specialized or secondary metabolites. NPs show interesting biological activities and many of them have been developed into essential medicines, including antibiotics (penicillin, streptomycin), anti-cancer drugs (bleomycin, doxorubicin), or cholesterol-lowering agents (lovastatin). This makes NPs and their encoding BGCs highly relevant from both a commercial and scientific perspective.

Information

Usage

See which versions are available: 

$ module avail antismash

Load one version into your environment and run it: 

$ module load antismash/7.0.0
$ run_antismash <input file> <output directory> [antismash options]

Note: The run_antismash helper script only covers basic usage. Because Antismash is installed in a dedicated "container" environment using Apptainer (similar to Docker, but more suited to HPC environments), more advanced usage will require a different invocation via Apptainer, for example: 

$ apptainer exec /export/apps/antismash/7.0.0/antismash.sif antismash \
        ${dir}/${strain_file}/Reference/Genome/*ctg.fa \
        --output-dir ${out_dir} \
        --taxon fungi \
        --cassis \
        --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go \
        --output-basename ${strain_file}_antismash \
        --genefinding-gff3 ${dir}/${strain_file}/${strain_file}_EIv1.release.gff3 \
        --allow-long-headers \
        -v \
        -c ${SLURM_CPUS_PER_TASK}

Note: of course you need to pay attention to the variables and bind your inputs into the container…

Installation

Notes from the sysadmin during installation: 

$ export APPTAINER_TMPDIR=/var/scratch/aorth
$ mkdir $APPTAINER_TMPDIR
$ apptainer pull /var/scratch/antismash.sif docker://antismash/standalone:7.0.0
$ curl -q https://dl.secondarymetabolites.org/releases/latest/docker-run_antismash-full > run_antismash
$ vim run_antismash # edit to use Apptainer instead of Docker
$ chmod +x run_antismash
$ sudo mkdir -p /export/apps/antismash/7.0.0/bin
$ sudo cp antismash.sif /export/apps/antismash/7.0.0
$ sudo cp run_antismash /export/apps/antismash/7.0.0/bin

Run the sample Streptomyces coelicolor genome: 

$ wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/203/835/GCF_000203835.1_ASM20383v1/GCF_000203835.1_ASM20383v1_genomic.gbff.gz
$ gunzip GCF_000203835.1_ASM20383v1_genomic.gbff.gz
$ mkdir -p /var/scratch/aorth/antismash
$ run_antismash GCF_000203835.1_ASM20383v1_genomic.gbff /var/scratch/aorth/antismash -c 4