positional arguments:

systems

The systems to detect. This is an obligatory option with no keyword associated to it. To detect all the protein secretion systems and related appendages: set to "all" (case insensitive). Otherwise, a single or multiple systems can be specified. For example: "T2SS T4P".

optional arguments:

-h, --help

show this help message and exit

Input dataset options:

--sequence-db SEQUENCE_DB

Path to the sequence dataset in fasta format.

--db-type {unordered_replicon,ordered_replicon,gembase,unordered}

The type of dataset to deal with. "unordered_replicon" corresponds to a non-assembled genome, "unordered" to a metagenomic dataset, "ordered_replicon" to an assembled genome, and "gembase" to a set of replicons where sequence identifiers follow this convention: ">RepliconName SequenceID".

--replicon-topology {linear,circular}

The topology of the replicons (this option is meaningful only if the db_type is 'ordered_replicon' or 'gembase'.

--topology-file TOPOLOGY_FILE

Topology file path. The topology file allows one to specify a topology (linear or circular) for each replicon (this option is meaningful only if the db_type is 'ordered_replicon' or 'gembase'. A topology file is a tabular file with two columns: the 1st is the replicon name, and the 2nd the corresponding topology: "RepliconA linear"

--idx

Forces to build the indexes for the sequence dataset even if they were presviously computed and present at the dataset location (default = False)

Systems detection options:

--inter-gene-max-space INTER_GENE_MAX_SPACE INTER_GENE_MAX_SPACE

Co-localization criterion: maximum number of components non-matched by a profile allowed between two matched components for them to be considered contiguous. Option only meaningful for 'ordered' datasets. The first value must match to a system, the second to a number of components. This option can be repeated several times: "--inter-gene-max-space T2SS 12 --inter-gene-max-space Flagellum 20"

--min-mandatory-genes-required MIN_MANDATORY_GENES_REQUIRED MIN_MANDATORY_GENES_REQUIRED

The minimal number of mandatory genes required for system assessment. The first value must correspond to a system name, the second value to an integer. This option can be repeated several times: "--minmandatory-genes-required T2SS 15 --min-mandatorygenes-required Flagellum 10"

--min-genes-required MIN_GENES_REQUIRED MIN_GENES_REQUIRED

The minimal number of genes required for system assessment (includes both 'mandatory' and 'accessory' components). The first value must correspond to a system name, the second value to an integer. This option can be repeated several times: "--min-genesrequired T2SS 15 --min-genes-required Flagellum 10"

--max-nb-genes MAX_NB_GENES MAX_NB_GENES

The maximal number of genes required for system assessment. The first value must correspond to a system name, the second value to an integer. This option can be repeated several times: "--max-nb-genes T2SS 5 --max-nb-genes Flagellum 10

--multi-loci MULTI_LOCI

Allow the storage of multi-loci systems for the specified systems. The systems are specified as a comma separated list (--multi-loci sys1,sys2) default is False

Options for Hmmer execution and hits filtering:

--hmmer HMMER_EXE

Path to the Hmmer program.

--index-db INDEX_DB_EXE

The indexer to be used for Hmmer. The value can be either 'makeblastdb' or 'formatdb' or the path to one of these binary (default = makeblastb)

--e-value-search E_VALUE_RES

Maximal e-value for hits to be reported during Hmmer search. (default = 1)

--i-evalue-select I_EVALUE_SEL

Maximal independent e-value for Hmmer hits to be selected for system detection. (default = 0.001)

--coverage-profile COVERAGE_PROFILE

Minimal profile coverage required in the hit alignment to allow the hit selection for system detection. (default = 0.5)

Path options:

-d DEF_DIR, --def DEF_DIR

Path to the systems definition files.

-o OUT_DIR, --out-dir OUT_DIR

Path to the directory where to store results. if outdir is specified res-search-dir will be ignored.

-r RES_SEARCH_DIR, --res-search-dir RES_SEARCH_DIR

Path to the directory where to store MacSyFinder search results directories (default current working directory).

--res-search-suffix RES_SEARCH_SUFFIX

The suffix to give to Hmmer raw output files.

--res-extract-suffix RES_EXTRACT_SUFFIX

The suffix to give to filtered hits output files.

-p PROFILE_DIR, --profile-dir PROFILE_DIR

Path to the profiles directory.

--profile-suffix PROFILE_SUFFIX

The suffix of profile files. For each 'Gene' element, the corresponding profile is searched in the 'profile_dir', in a file which name is based on the Gene name + the profile suffix. For instance, if the Gene is named 'gspG' and the suffix is '.hmm3', then the profile should be placed at the specified location and be named 'gspG.hmm3'

General options:

-w WORKER_NB, --worker WORKER_NB

Number of workers to be used by MacSyFinder. In the case the user wants to run MacSyFinder in a multithread mode. (0 mean all cores will be used, default 1)

-v, --verbosity

Increases the verbosity level. There are 4 levels: Error messages (default), Warning (-v), Info (-vv) and Debug.(-vvv)

--log LOG_FILE

Path to the directory where to store the 'macsyfinder.log' log file.

--config CFG_FILE

Path to a putative MacSyFinder configuration file to be used.

--previous-run PREVIOUS_RUN

Path to a previous MacSyFinder run directory. It allows one to skip the Hmmer search step on same dataset, as it uses previous run results and thus parameters regarding Hmmer detection. The configuration file from this previous run will be used. (conflict with options --config, --sequence-db, --profile-suffix, --resextract-suffix, --e-value-res, --db-type, --hmmer)

For more details, visit the MacSyFinder website and see the MacSyFinder documentation.