Command Line Use

Note: These are instructions for the soon-to-be-released antiSMASH version 5. antiSMASH 4 command line options are slightly different. Use antismash --help-showall to get help for version 4.

The antiSMASH command line tool comes with a built-in help system. Use antismash --help to display help for the most common options, or antismash --help-showall to get a description of all possible options.

Fast run

Running antismash without parameters will run the core detection modules and all fast cluster-specific analysis steps. More time-consuming options such as the ClusterBlast analyses, cluster-based PFAM annotations, smCoG tree generation, etc. will not be run. On a quad-core machine, running the Streptomyces coelicolor genome with these options will take about two minutes.

This is how the antiSMASH web service runs fast mode jobs from https://fast.antismash.secondarymetabolites.org/

Example:

antismash streptomyces_coelicolor.gbk

Minimal run

Running antismash with the --minimal parameter will only run the core detection modules, none of the cluster-specific analysis steps. On a quad-core machine, running the Streptomyces coelicolor genome in minimal mode will take about one minute. In general, we recommend running without the --minimal option, as a default fast run will generate much more useful results for only one additional minute of runtime.

Example:

antismash --minimal streptomyces_coelicolor.gbk

On a quad core machine, running all these options for the Streptomyces coelicolor genome will take a bit over 20 minutes.

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