# antiSMASH 6.0.1 ## 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: ```console bash source /local/cluster/antismash/activate.sh ``` 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: ```console $ which antismash /local/cluster/antismash/bin/antismash $ antismash --version antiSMASH 6.0.1 ``` help message: ```console $ 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 records (default: -1). -1 to disable --minlength MINLENGTH Only process sequences larger than (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 ``` 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/ ```console 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. ```console antismash --minimal streptomyces_coelicolor.gbk ``` ### Full-featured run On a quad core machine, running all these options for the Streptomyces coelicolor genome will take a bit over 20 minutes. ```console antismash --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go --smcog-trees streptomyces_coelicolor.gbk ``` software ref: software ref: research ref: