Command-line parameters

Run pixi run ssuextract --help for the installed version's generated help.

Parameter	Default	Description
-q, --query	data/example	One .fna, .fa, or .fasta file, or a directory containing those files. The short form is available through pixi run ssuextract.
--modeldir	resources/models	Directory containing Infernal covariance models.
--outdir	results/<input-name>	Output directory. The input name is the directory name or FASTA file stem.
--database_path	Configured path or resources/database	Root containing database profiles.
--database_profile	Saved profile or curated	Profile name: curated or img. The option overrides the saved profile for one run.
--model_marker_map	config/model_markers.json	Covariance-model to marker mapping.
--max_blast_targets	500	Candidate policy limit; one extra hit is fetched as a truncation sentinel.
--top_hits	5	Number of ranked BLAST subjects reported per query. Equal-best assignment subjects and the best IMG, PR2, and SILVA subjects among the fetched candidates are retained below this cutoff.
--tree_classification	off	Use a query-plus-reference tree for taxonomy assignment.
--tree_reference_count	100	Unique BLAST reference sequences aligned with each query in tree mode.
--tree_assignment_neighbors	5	Nearest named tree references used for the taxonomy LCA.
--tree_trim_gap_fraction	0.9	After masking covariance-model insert columns, remove match columns with a larger gap fraction.
--min_extract_length	500	Minimum accepted hit length in nucleotides; 0 disables the filter.
--threads_per_job	2	CPUs assigned to each Infernal, BLAST, or cmalign task. IQ-TREE uses one thread for reproducible neighbor ordering.
--max_cpus	16	Maximum CPUs assigned to one Nextflow task.
--max_memory	128.GB	Maximum memory assigned to one Nextflow task.
--max_time	240.h	Maximum wall time assigned to one Nextflow task.

Pixi commands

Command	Effect
pixi run setup	Select, install, validate, or update a database profile.
pixi run setup --database_profile img	Install or inspect the IMG profile without the profile prompt.
pixi run setup --database_profile curated --update	Install the latest verified curated profile without an update prompt.
pixi run example	Run the bundled assemblies.
pixi run ssuextract	Run the pipeline with supplied Nextflow arguments.
pixi run test	Run unit, integration, profile-routing, and version checks.
pixi run dryrun	Preview the Nextflow graph without executing tasks.