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
--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
--help-showall to get a description of all possible options.
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/
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
option, as a default fast run will generate much more useful results for only
one additional minute of runtime.
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