qa
Assess bins for contamination and completeness.
Estimates the completeness, contamination, and strain heterogeneity of each bin from the marker genes
identified by the analyze command, and reports the results in one of several
tables. The qa command must be given the marker file and output folder used with analyze. The
lineage_wf and taxonomy_wf commands write their
marker file to the output folder (lineage.ms.gz or <taxon>.ms.gz), so qa can be re-run on the
output of a workflow to produce other tables. The marker file can be given with or without the .gz
extension (e.g. ./output/lineage.ms).
The -o, --out_format option specifies the desired output (see qa output formats):
summary of bin completeness, contamination, and strain heterogeneity
extended summary of bin quality (includes GC, genome size, coding density, …)
summary of bin quality for increasingly basal lineage-specific marker sets
list of marker genes for each bin along with the number of times each marker was identified
list of bin ID, marker gene ID, and called gene ID for each identified marker gene
list of marker genes present multiple times in a bin
list of marker genes present multiple times on the same scaffold
list indicating the position of each marker gene within a bin
FASTA file of marker genes identified in each bin
The statistics reported in these tables are described in Reported statistics.
Other options:
--exclude_markers: file specifying markers to exclude from marker sets. Each marker to exclude should be listed on a separate line of the file.--individual_markers: treat markers as independent (i.e., ignore the co-located set structure).--skip_adj_correction: do not combine hits to adjacent genes (see note below).--skip_pseudogene_correction: do not filter hits that are likely to be pseudogenes. By default, hits with an alignment shorter than 30% of the length of the marker HMM are ignored.--aai_strain: amino acid identity (AAI) threshold used to identify strain heterogeneity.-a, --alignment_file: produce a file showing the alignment of multi-copy genes and their AAI, which can be used to further assess strain heterogeneity.--ignore_thresholds: ignore model-specific score thresholds.-e, --e_value: e-value cut-off (not used if model-specific thresholds are specified).-l, --length: minimum alignment length as a fraction of the marker HMM length (not used if model-specific thresholds are specified).-c, --coverage_file: file containing the coverage of each sequence; coverage information is appended to table type 2 when this file is provided (see coverage).-f, --file: print results to file instead of the console.--tab_table: for tabular outputs, print a tab-separated values table instead of a table formatted for console output.
Note
Adjacent called genes matching the same marker gene may indicate a true duplication event, a gene calling
error, or an assembly error. Unless --skip_adj_correction is used, hits to the same marker gene on a
run of consecutive genes of a scaffold are combined into a single hit, so they are not treated as
contamination. The IDs of the combined genes are joined with a pair of ampersands (&&). Output
format 7 lists marker genes present multiple times on the same scaffold, which is useful for identifying
true gene duplication events, gene calling errors, or assembly errors.
Arguments
usage: checkm qa [-h] [-o {1,2,3,4,5,6,7,8,9}] [--exclude_markers EXCLUDE_MARKERS]
[--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] [-f FILE] [--tab_table] [-t THREADS] [-q]
[--tmpdir TMPDIR]
marker_file analyze_dir
Assess bins for contamination and completeness.
positional arguments:
marker_file marker file specified during analyze command
analyze_dir directory specified during analyze command
options:
-h, --help show this help message and exit
-o, --out_format {1,2,3,4,5,6,7,8,9}
desired output: (default: 1)
1. summary of bin completeness and contamination
2. extended summary of bin statistics (includes GC, genome size, ...)
3. summary of bin quality for increasingly basal lineage-specific marker sets
4. list of marker genes and their counts
5. list of bin id, marker gene id, gene id
6. list of marker genes present multiple times in a bin
7. list of marker genes present multiple times on the same scaffold
8. list indicating position of each marker gene within a bin
9. FASTA file of marker genes identified in each bin
--exclude_markers EXCLUDE_MARKERS
file specifying markers to exclude from marker sets
--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)
-f, --file FILE print results to file (default: stdout)
--tab_table print tab-separated values table
-t, --threads THREADS
number of threads (default: 1)
-q, --quiet suppress console output
--tmpdir TMPDIR specify an alternative directory for temporary files
Note: lineage_wf and taxonomy_wf produce a marker file in the specified output directory. The
lineage workflow produces a marker file called lineage.ms.gz, while the taxonomy workflow
produces a marker file called <taxon>.ms.gz (e.g. Bacteria.ms.gz). Marker files can be
given with or without the .gz extension (e.g. lineage.ms).
Example: checkm qa ./output/lineage.ms ./output
Example
checkm qa ./output/lineage.ms ./output
checkm qa -o 2 --tab_table -f qa_extended.tsv ./output/lineage.ms ./output