lineage_wf

Runs tree, lineage_set, analyze, qa.

Runs the lineage-specific workflow, which consists of the tree, lineage_set, analyze, and qa commands. This is the recommended workflow for assessing the completeness and contamination of genome bins. 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 lineage.ms.gz is also written to the output folder, and the qa command can be re-run on the output folder to produce other tables:

checkm qa -o 1 ./output/lineage.ms ./output

• --rm_tmp_files: remove the bins and storage folders once quality_report.tsv has been written. This saves disk space, but qa and the plotting commands can then no longer be run on the output folder. A folder containing the input genomes is never removed.

• --gplace_max_memory: limit the memory used to place bins in the reference genome tree (see tree and System requirements).

Note

CheckM <= 1.2.10 printed the qa -o 1 table to the console (or to the file given with -f, as a tab-separated table with --tab_table). These options, and --reduced_tree and --pplacer_threads, were removed in CheckM 1.3.0.

Arguments

usage: checkm lineage_wf [-h] [--ali] [--nt] [-g] [-u UNIQUE] [-m MULTI] [--force_domain]
                         [--no_refinement] [--individual_markers] [--skip_adj_correction]
                         [--skip_pseudogene_correction] [--aai_strain AAI_STRAIN]
                         [-a ALIGNMENT_FILE] [--ignore_thresholds] [-e E_VALUE] [-l LENGTH]
                         [--rm_tmp_files] [-x EXTENSION] [-t THREADS] [--gplace_max_memory MEMORY]
                         [-q] [--tmpdir TMPDIR]
                         bin_input output_dir

Runs tree, lineage_set, analyze, qa

positional arguments:
  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
  -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
  --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)
  --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)
  --gplace_max_memory MEMORY
                        memory gPlace may use to place bins, e.g. 64G or 500M (a plain number is GiB) [default: set by gPlace from the available memory]
  -q, --quiet           suppress console output
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm lineage_wf ./bins ./output

Example

checkm lineage_wf -t 8 -x fa ./bins ./output
checkm lineage_wf -t 8 -x fa --rm_tmp_files ./bins ./output
checkm lineage_wf -t 8 -x fa --gplace_max_memory 8G ./bins ./output