checkm
Tags: assembly-quality microbial-genomes completeness contamination bactopia-tool
Assessment of microbial genome assembly quality.
This Bactopia Tool uses CheckM to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes using a set of lineage-specific marker genes.
Usage
Bactopia CLI:
bactopia --wf checkm \
--bactopia /path/to/your/bactopia/results
Nextflow:
nextflow run bactopia/bactopia/workflows/bactopia-tools/checkm/main.nf \
--bactopia /path/to/your/bactopia/results
Outputs
Expected Output Files
<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│ └── tools
│ └── checkm-<TIMESTAMP>
│ ├── <SAMPLE_NAME>.tsv
│ ├── logs
│ │ ├── checkm.log
│ │ ├── nf.command.{begin,err,log,out,run,sh,trace}
│ │ └── versions.yml
│ └── supplemental
│ ├── <SAMPLE_NAME>-genes.aln
│ ├── bins
│ │ └── <SAMPLE_NAME>
│ │ ├── genes.faa.gz
│ │ ├── genes.gff
│ │ ├── hmmer.analyze.txt.gz
│ │ └── hmmer.tree.txt
│ ├── lineage.ms
│ └── storage
│ ├── aai_qa
│ ├── bin_stats.analyze.tsv
│ ├── bin_stats.tree.tsv
│ ├── bin_stats_ext.tsv
│ ├── checkm_hmm_info.pkl.gz
│ ├── marker_gene_stats.tsv
│ ├── phylo_hmm_info.pkl.gz
│ └── tree
│ ├── PF00164.20.masked.faa.gz
│ ├── PF00177.16.masked.faa.gz
│ ├── PF00181.18.masked.faa.gz
│ ├── PF00189.15.masked.faa.gz
│ ├── PF00203.16.masked.faa.gz
│ ├── PF00237.14.masked.faa.gz
│ ├── PF00238.14.masked.faa.gz
│ ├── PF00252.13.masked.faa.gz
│ ├── PF00276.15.masked.faa.gz
│ ├── PF00281.14.masked.faa.gz
│ ├── PF00333.15.masked.faa.gz
│ ├── PF00366.15.masked.faa.gz
│ ├── PF00410.14.masked.faa.gz
│ ├── PF00411.14.masked.faa.gz
│ ├── PF00562.23.masked.faa.gz
│ ├── PF00623.15.masked.faa.gz
│ ├── PF00673.16.masked.faa.gz
│ ├── PF00831.18.masked.faa.gz
│ ├── PF00861.17.masked.faa.gz
│ ├── PF03719.10.masked.faa.gz
│ ├── PF03947.13.masked.faa.gz
│ ├── PF04560.15.masked.faa.gz
│ ├── PF04561.9.masked.faa.gz
│ ├── PF04565.11.masked.faa.gz
│ ├── PF04997.7.masked.faa.gz
│ ├── PF11987.3.masked.faa.gz
│ ├── concatenated.fasta.gz
│ ├── concatenated.pplacer.json
│ ├── concatenated.tre
│ └── pplacer.out
└── bactopia-runs
└── checkm-<TIMESTAMP>
├── merged-results
│ ├── checkm.tsv
│ └── logs
│ └── checkm-concat
│ ├── nf.command.{begin,err,log,out,run,sh,trace}
│ └── versions.yml
└── nf-reports
├── checkm-dag.dot
├── checkm-report.html
└── checkm-timeline.html
Quality Assessment
| File | Description |
|---|---|
*.genes.aln | Alignment of multi-copy genes and their AAI identity |
*.results.txt | Final results of CheckM's lineage_wf |
lineage.ms | Output file describing marker set for each bin |
bins/** | Directory with inputs for processing by CheckM |
storage/** | Directory with intermediate results from CheckM processing |
Merged Results
| File | Description |
|---|---|
checkm.tsv | Merged TSV file with CheckM results from all samples |
Audit Trail
Below are files that can assist you in understanding which parameters and program versions were used.
Logs
Each process that is executed will have a folder named logs. In this folder are helpful
files for you to review if the need ever arises.
| Extension | Description |
|---|---|
| .begin | An empty file used to designate the process started |
| .err | Contains STDERR outputs from the process |
| .log | Contains both STDERR and STDOUT outputs from the process |
| .out | Contains STDOUT outputs from the process |
| .run | The script Nextflow uses to stage/unstage files and queue processes based on given profile |
| .sh | The script executed by bash for the process |
| .trace | The Nextflow trace report for the process |
| versions.yml | A YAML formatted file with program versions |
Nextflow Reports
These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.
| Filename | Description |
|---|---|
| checkm-dag.dot | The Nextflow DAG visualization |
| checkm-report.html | The Nextflow Execution Report |
| checkm-timeline.html | The Nextflow Timeline Report |
| checkm-trace.txt | The Nextflow Trace report |
Parameters
Required Parameters
Define where the pipeline should find input data and save output data.
| Parameter | Type | Default | Description |
|---|---|---|---|
--bactopia | string | The path to bactopia results to use as inputs |
CheckM Parameters
| Parameter | Type | Default | Description |
|---|---|---|---|
--checkm_unique | integer | 10 | Minimum number of unique phylogenetic markers required to use lineage-specific marker set. |
--checkm_multi | integer | 10 | Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set. |
--checkm_aai_strain | number | 0.9 | AAI threshold used to identify strain heterogeneity |
--checkm_length | number | 0.7 | Percent overlap between target and query |
Filtering Parameters
Use these parameters to specify which samples to include or exclude.
| Parameter | Type | Default | Description |
|---|---|---|---|
--include | string | A text file containing sample names (one per line) to include from the analysis | |
--exclude | string | A text file containing sample names (one per line) to exclude from the analysis |
Optional Parameters
These optional parameters can be useful in certain settings.
| Parameter | Type | Default | Description |
|---|---|---|---|
--outdir | string | bactopia | Base directory to write results to |
Nextflow Profile Parameters
Parameters to fine-tune your Nextflow setup.
| Parameter | Type | Default | Description |
|---|---|---|---|
--datasets_cache | string | <HOME>/.bactopia/datasets | Directory where downloaded datasets should be stored. |
Helpful Parameters
Uncommonly used parameters that might be useful.
| Parameter | Type | Default | Description |
|---|---|---|---|
--wf | string | bactopia | Specify which workflow or Bactopia Tool to execute |
--list_wfs | boolean | List the available workflows and Bactopia Tools to use with '--wf' | |
--help_all | boolean | An alias for --help --show_hidden_params | |
--version | boolean | Display version text. |
Composition
This workflow uses the following subworkflows:
- checkm - Assess metagenome bin completeness using CheckM.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
CheckM
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043-1055 (2015)