taxon_set

Generate a taxonomic-specific marker set.

Writes the marker set for the specified taxon to a marker file, which is used by the analyze and qa commands (see Taxonomic-specific workflow). Use taxon_list to see the available taxa. The marker file is gzip-compressed, and .gz is appended to its name if not already present (e.g., bacteria.ms is written as bacteria.ms.gz); later commands accept the name with or without .gz.

• rank: taxonomic rank of the desired taxonomic-specific marker set (e.g., domain)

• taxon: taxon of interest (e.g., Bacteria)

• marker_file: output file describing the taxonomic-specific marker set

Arguments

usage: checkm taxon_set [-h] [-q] [--tmpdir TMPDIR]
                        {life,domain,phylum,class,order,family,genus,species} taxon marker_file

Generate taxonomic-specific marker set.

positional arguments:
  {life,domain,phylum,class,order,family,genus,species}
                        taxonomic rank
  taxon                 taxon of interest
  marker_file           output file describing taxonomic-specific marker set (gzip-compressed; '.gz' is appended if not present)

options:
  -h, --help            show this help message and exit
  -q, --quiet           suppress console output
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm taxon_set domain Bacteria bacteria.ms

Example

checkm taxon_set domain Bacteria bacteria.ms
checkm taxon_set phylum Cyanobacteria cyanobacteria.ms