antiSMASH
antiSMASH allows the rapid genome-wide identification, annotation and analysis
of secondary metabolite biosynthesis gene clusters in bacterial and fungal
genomes. It integrates and cross-links with a large number of in silico
secondary metabolite analysis tools that have been published earlier.
To activate:
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bash
source /local/cluster/antismash/activate.sh
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To use in SGE:
Make a bash script and put the source /local/cluster/antismash/activate.sh
before your antismash commands, and submit the script using SGE_Batch or
SGE_Array.
Location and version:
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$ which antismash
/local/cluster/antismash/bin/antismash
$ antismash --version
antiSMASH 6.0.1
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help message:
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$ antismash --help-showall
########### antiSMASH 6.0.1 #############
usage: antismash [--taxon {bacteria,fungi}] [--output-dir OUTPUT_DIR]
[--output-basename OUTPUT_BASENAME] [--reuse-results PATH] [--limit LIMIT]
[--minlength MINLENGTH] [--start START] [--end END] [--databases PATH]
[--write-config-file PATH] [--without-fimo]
[--executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,...] [--allow-long-headers]
[-v] [-d] [--logfile PATH] [--list-plugins] [--check-prereqs]
[--limit-to-record RECORD_ID] [-V] [--profiling] [--skip-sanitisation]
[--skip-zip-file] [--minimal] [--enable-genefunctions] [--enable-tta]
[--enable-lanthipeptides] [--enable-thiopeptides] [--enable-nrps-pks]
[--enable-sactipeptides] [--enable-lassopeptides] [--enable-t2pks] [--enable-html]
[--genefinding-tool {glimmerhmm,prodigal,prodigal-m,none,error}]
[--genefinding-gff3 GFF3_FILE] [--hmmdetection-strictness {strict,relaxed,loose}]
[--fullhmmer] [--fullhmmer-pfamdb-version FULLHMMER_PFAMDB_VERSION] [--cassis]
[--clusterhmmer] [--clusterhmmer-pfamdb-version CLUSTERHMMER_PFAMDB_VERSION]
[--sideload JSON] [--sideload-simple ACCESSION:START-END] [--tigrfam]
[--smcog-trees] [--tta-threshold TTA_THRESHOLD] [--cb-general] [--cb-subclusters]
[--cb-knownclusters] [--cb-nclusters count] [--cb-min-homology-scale LIMIT] [--asf]
[--pfam2go] [--rre] [--rre-cutoff RRE_CUTOFF] [--rre-minlength RRE_MIN_LENGTH]
[--cc-mibig] [--cc-custom-dbs FILE1,FILE2,...] [--html-title HTML_TITLE]
[--html-description HTML_DESCRIPTION] [--html-start-compact] [-h] [--help-showall]
[-c CPUS]
[SEQUENCE [SEQUENCE ...]]
arguments:
SEQUENCE GenBank/EMBL/FASTA file(s) containing DNA.
--------
Options
--------
-h, --help Show this help text.
--help-showall Show full lists of arguments on this help text.
-c CPUS, --cpus CPUS How many CPUs to use in parallel. (default: 64)
Basic analysis options:
--taxon {bacteria,fungi}
Taxonomic classification of input sequence. (default: bacteria)
Additional analysis:
--fullhmmer Run a whole-genome HMMer analysis.
--cassis Motif based prediction of SM gene cluster regions.
--clusterhmmer Run a cluster-limited HMMer analysis.
--tigrfam Annotate clusters using TIGRFam profiles.
--smcog-trees Generate phylogenetic trees of sec. met. cluster orthologous groups.
--tta-threshold TTA_THRESHOLD
Lowest GC content to annotate TTA codons at (default: 0.65).
--cb-general Compare identified clusters against a database of antiSMASH-predicted
clusters.
--cb-subclusters Compare identified clusters against known subclusters responsible for
synthesising precursors.
--cb-knownclusters Compare identified clusters against known gene clusters from the MIBiG
database.
--asf Run active site finder analysis.
--pfam2go Run Pfam to Gene Ontology mapping module.
--rre Run RREFinder precision mode on all RiPP gene clusters.
--cc-mibig Run a comparison against the MIBiG dataset
Output options:
--output-dir OUTPUT_DIR
Directory to write results to.
--output-basename OUTPUT_BASENAME
Base filename to use for output files within the output directory.
--html-title HTML_TITLE
Custom title for the HTML output page (default is input filename).
--html-description HTML_DESCRIPTION
Custom description to add to the output.
--html-start-compact Use compact view by default for overview page.
Advanced options:
--reuse-results PATH Use the previous results from the specified json datafile
--limit LIMIT Only process the first <limit> records (default: -1). -1 to disable
--minlength MINLENGTH
Only process sequences larger than <minlength> (default: 1000).
--start START Start analysis at nucleotide specified.
--end END End analysis at nucleotide specified
--databases PATH Root directory of the databases (default:
/local/cluster/antismash-6.0.1/lib/python3.8/site-
packages/antismash/databases).
--write-config-file PATH
Write a config file to the supplied path
--without-fimo Run without FIMO (lowers accuracy of RiPP precursor predictions)
--executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,...
A comma separated list of executable name->path pairs to override any on the
system path.E.g. diamond=/alternate/path/to/diamond,hmmpfam2=hmm2pfam
--allow-long-headers Prevents long headers from being renamed
--hmmdetection-strictness {strict,relaxed,loose}
Defines which level of strictness to use for HMM-based cluster detection,
(default: relaxed).
--sideload JSON Sideload annotations from the JSON file in the given paths. Multiple files
can be provided, separated by a comma.
--sideload-simple ACCESSION:START-END
Sideload a single subregion in record ACCESSION from START to END. Positions
are expected to be 0-indexed, with START inclusive and END exclusive.
Debugging & Logging options:
-v, --verbose Print verbose status information to stderr.
-d, --debug Print debugging information to stderr.
--logfile PATH Also write logging output to a file.
--list-plugins List all available sec. met. detection modules.
--check-prereqs Just check if all prerequisites are met.
--limit-to-record RECORD_ID
Limit analysis to the record with ID record_id
-V, --version Display the version number and exit.
--profiling Generate a profiling report, disables multiprocess python.
--skip-sanitisation Skip input record sanitisation. Use with care.
--skip-zip-file Do not create a zip of the output
Debugging options for cluster-specific analyses:
--minimal Only run core detection modules, no analysis modules unless explicitly
enabled
--enable-genefunctions
Enable Gene function annotations (default: enabled, unless --minimal is
specified)
--enable-tta Enable TTA detection (default: enabled, unless --minimal is specified)
--enable-lanthipeptides
Enable Lanthipeptides (default: enabled, unless --minimal is specified)
--enable-thiopeptides
Enable Thiopeptides (default: enabled, unless --minimal is specified)
--enable-nrps-pks Enable NRPS/PKS analysis (default: enabled, unless --minimal is specified)
--enable-sactipeptides
Enable sactipeptide detection (default: enabled, unless --minimal is
specified)
--enable-lassopeptides
Enable lassopeptide precursor prediction (default: enabled, unless --minimal
is specified)
--enable-t2pks Enable type II PKS analysis (default: enabled, unless --minimal is specified)
--enable-html Enable HTML output (default: enabled, unless --minimal is specified)
Gene finding options (ignored when ORFs are annotated):
--genefinding-tool {glimmerhmm,prodigal,prodigal-m,none,error}
Specify algorithm used for gene finding: GlimmerHMM, Prodigal, Prodigal
Metagenomic/Anonymous mode, or none. The 'error' option will raise an error
if genefinding is attempted. The 'none' option will not run genefinding.
(default: error).
--genefinding-gff3 GFF3_FILE
Specify GFF3 file to extract features from.
Full HMMer options:
--fullhmmer-pfamdb-version FULLHMMER_PFAMDB_VERSION
PFAM database version number (e.g. 27.0) (default: latest).
Cluster HMMer options:
--clusterhmmer-pfamdb-version CLUSTERHMMER_PFAMDB_VERSION
PFAM database version number (e.g. 27.0) (default: latest).
TIGRFam options:
NRPS/PKS options:
ClusterBlast options:
--cb-nclusters count Number of clusters from ClusterBlast to display, cannot be greater than 50.
(default: 10)
--cb-min-homology-scale LIMIT
A minimum scaling factor for the query BGC in ClusterBlast results. Valid
range: 0.0 - 1.0. Warning: some homologous genes may no longer be visible!
(default: 0.0)
RREfinder options:
--rre-cutoff RRE_CUTOFF
Bitscore cutoff for RRE pHMM detection (default: 25.0).
--rre-minlength RRE_MIN_LENGTH
Minimum amino acid length of RRE domains (default: 50).
ClusterCompare options:
--cc-custom-dbs FILE1,FILE2,...
A comma separated list of database config files to run with
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Usage:
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/
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antismash streptomyces_coelicolor.gbk
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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.
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antismash --minimal streptomyces_coelicolor.gbk
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Full-featured run
On a quad core machine, running all these options for the Streptomyces
coelicolor genome will take a bit over 20 minutes.
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antismash --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go --smcog-trees streptomyces_coelicolor.gbk
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software ref: https://docs.antismash.secondarymetabolites.org
software ref: https://antismash.secondarymetabolites.org
research ref: https://doi.org/10.1093/nar/gkab335