lineage_set

Infer lineage-specific marker sets for each bin.

This step of the lineage-specific workflow uses the placement of each bin in the reference genome tree, as determined by the tree command, to infer a lineage-specific marker set for each bin. The marker sets are written to the specified marker file, which is used by the analyze and qa commands. The marker file is gzip-compressed, and .gz is appended to its name if not already present (e.g., lineage.ms is written as lineage.ms.gz); later commands accept the name with or without .gz.

• -u, --unique: minimum number of unique phylogenetic markers required to use a lineage-specific marker set, otherwise a domain-level marker set is used.

• -m, --multi: maximum number of multi-copy phylogenetic markers before defaulting to a domain-level marker set.

• --force_domain: use domain-level marker sets for all bins.

• --no_refinement: do not perform lineage-specific marker set refinement.

Arguments

usage: checkm lineage_set [-h] [-u UNIQUE] [-m MULTI] [--force_domain] [--no_refinement] [-q]
                          [--tmpdir TMPDIR]
                          tree_dir marker_file

Infer lineage-specific marker sets for each bin.

positional arguments:
  tree_dir             directory specified during tree command
  marker_file          output file describing marker set for each bin (gzip-compressed; '.gz' is appended if not present)

options:
  -h, --help           show this help message and exit
  -u, --unique UNIQUE  minimum number of unique phylogenetic markers required to use lineage-specific marker set (default: 10)
  -m, --multi MULTI    maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set (default: 10)
  --force_domain       use domain-level sets for all bins
  --no_refinement      do not perform lineage-specific marker set refinement
  -q, --quiet          suppress console output
  --tmpdir TMPDIR      specify an alternative directory for temporary files

Example: checkm lineage_set ./output lineage.ms

Example

checkm lineage_set ./output ./output/lineage.ms