Command Line Use#
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.
Default run#
Running antiSMASH without parameters will run the core detection modules and those analyses which are quite fast to run.
More time consuming options such as the ClusterBlast analyses, 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.
Example:
antismash streptomyces_coelicolor.gbk
Minimal run#
Running antiSMASH with the --minimal parameter will only run the core detection modules and no other modules.
Any modules disabled by this (e.g. HTML output) can be explicitly re-enabled,
if desired, with their matching option (see --help-showall).
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 run will generate much more useful results for only
one additional minute of runtime.
Example:
antismash --minimal streptomyces_coelicolor.gbk
Reusing results from a previous run#
The JSON output file previously generated by antiSMASH can be reused to regenerate other output files. Additional analyses can be enabled for the new run by adding their options.
NOTE: there are some situations in which results cannot be reused, these are typically when detection modules have changed since the results were generated. In this case, using the version of antiSMASH that generated the results will be required.
Example:
antismash --reuse-results strepomyces_coelicolor.json
Customising output#
Output directories and custom names for output can be specified, instead of using the input filename by default
(see the --output family of arguments).
HTML output can also be customised with alternative titles and descriptions
(see the --html family of arguments).