CLI Options and Arguments

Command Modes

MirMachine supports these invocation modes:

MirMachine.py --node <text> --species <text> --genome <text> [options]
MirMachine.py --species <text> --genome <text> --family <text> [options]
MirMachine.py --node <text> [--add-all-nodes]
MirMachine.py --print-all-nodes
MirMachine.py --print-all-families
MirMachine.py --print-ascii-tree
MirMachine.py (-h | --help)
MirMachine.py --version

Run Examples

Node-based run:

MirMachine.py --node Caenorhabditis --species ce11 \
             --genome /path/to/genome.fa --model combined

Single-family run:

MirMachine.py --species ce11_let7 --genome /path/to/genome.fa \
             --family Let-7

Show families for a node:

MirMachine.py --node Caenorhabditis

Arguments

Short	Long	Description
-n	--node <text>	Node name (example: Caenorhabditis).
-s	--species <text>	Species/run label used in output filenames and YAML config.
-g	--genome <text>	Path to uncompressed genome FASTA.
-m	--model <text>	Model set: combined, proto, or deutero (default: combined).
-f	--family <text>	Search only one miRNA family (example: Let-7).
-e	--evalue <float>	Inclusion threshold passed to cmsearch --incE (default: 0.2).
-c	--cpu <integer>	Parallel jobs passed to Snakemake (default: 2).

Options

Flag	Description
-a, --add-all-nodes	Expand node query to include descendants (broader family set).
-o, --single-node-only	Limit searched families to only the selected node.
-p, --print-all-nodes	Print available node names and exit.
-l, --print-all-families	Print families available in each model and exit.
-t, --print-ascii-tree	Print an ASCII representation of the taxonomy tree and exit.
-u, --unlock	Unlock a stalled Snakemake working directory.
-r, --remove	Delete all generated output files tracked by the workflow.
-d, --dry	Dry-run the Snakemake DAG without executing jobs.
--touch	Mark targets as up-to-date without re-running jobs.
--long	Use long-miRNA covariance models from mirmachine/meta/lcms.
-h, --help	Show help text and exit.
--version	Show MirMachine version and exit.

Notes

• --family mode does not require --node.

• If --node is invalid, MirMachine prints valid nodes and exits.

• Model name validation is strict: combined, proto, deutero.