taxonomy_wf

Runs taxon_set, analyze, qa.

Runs the taxonomic-specific workflow, which consists of the taxon_set, analyze, and qa commands. All bins are assessed with the marker set of the specified taxon. Use taxon_list to see the available taxa. See the individual commands for a description of their options.

The results are written to quality_report.tsv in the output folder: the tab-separated table produced by qa -o 2 --tab_table (see Reported statistics). The marker file <taxon>.ms.gz (e.g. Bacteria.ms.gz) is also written to the output folder, so qa can be re-run to produce other tables.

• --rm_tmp_files: remove the bins and storage folders once quality_report.tsv has been written. qa and the plotting commands can then no longer be run on the output folder.

Note

CheckM <= 1.2.10 printed the qa -o 1 table to the console or to the file given with -f. The -f and --tab_table options were removed in CheckM 1.3.0.

Arguments

usage: checkm taxonomy_wf [-h] [--ali] [--nt] [-g] [--individual_markers] [--skip_adj_correction]
                          [--skip_pseudogene_correction] [--aai_strain AAI_STRAIN]
                          [-a ALIGNMENT_FILE] [--ignore_thresholds] [-e E_VALUE] [-l LENGTH]
                          [-c COVERAGE_FILE] [--rm_tmp_files] [-x EXTENSION] [-t THREADS] [-q]
                          [--tmpdir TMPDIR]
                          {life,domain,phylum,class,order,family,genus,species} taxon bin_input
                          output_dir

Runs taxon_set, analyze, qa

positional arguments:
  {life,domain,phylum,class,order,family,genus,species}
                        taxonomic rank
  taxon                 taxon of interest
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_dir            directory to write output files

options:
  -h, --help            show this help message and exit
  --ali                 generate HMMER alignment file for each bin
  --nt                  generate nucleotide gene sequences for each bin
  -g, --genes           bins contain genes as amino acids instead of nucleotide contigs
  --individual_markers  treat marker as independent (i.e., ignore co-located set structure)
  --skip_adj_correction
                        do not exclude adjacent marker genes when estimating contamination
  --skip_pseudogene_correction
                        skip identification and filtering of pseudogenes
  --aai_strain AAI_STRAIN
                        AAI threshold used to identify strain heterogeneity (default: 0.9)
  -a, --alignment_file ALIGNMENT_FILE
                        produce file showing alignment of multi-copy genes and their AAI identity
  --ignore_thresholds   ignore model-specific score thresholds
  -e, --e_value E_VALUE
                        e-value cut off (default: 1e-10)
  -l, --length LENGTH   minimum alignment length as a fraction of the marker HMM length (default: 0.7)
  -c, --coverage_file COVERAGE_FILE
                        file containing coverage of each sequence; coverage information added to table type 2 (see coverage command)
  --rm_tmp_files        remove the bins and storage directories once the quality report has been written
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm taxonomy_wf domain Bacteria ./bins ./output

Example

checkm taxonomy_wf domain Bacteria ./bins ./output
checkm taxonomy_wf phylum Cyanobacteria -t 8 -x fa ./bins ./output