Bactopia Tool - checkm

The checkm module is used CheckM to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Example Usage

bactopia --wf checkm \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt  

Output Overview

Below is the default output structure for the checkm tool. Where possible the file descriptions below were modified from a tools description.

checkm/
├── <SAMPLE_NAME>
│   ├── bins/
│   ├── logs
│   │   └── checkm
│   │       ├── nf-checkm.{begin,err,log,out,run,sh,trace}
│   │       ├── checkm.log
│   │       └── versions.yml
│   ├── storage/
│   ├── lineage.ms
│   ├── <SAMPLE_NAME>-genes.aln
│   └── <SAMPLE_NAME>-results.txt
├── checkm.tsv
├── logs
│   ├── csvtk_concat
│   │   ├── nf-csvtk_concat.{begin,err,log,out,run,sh,trace}
│   │   └── versions.yml
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions.{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├── checkm-dag.dot
│   ├── checkm-report.html
│   ├── checkm-timeline.html
│   └── checkm-trace.txt
├── software_versions.yml
└── software_versions_mqc.yml

Results

CheckM

Below is a description of the per-sample results from CheckM.

Filename	Description
bins/	A folder with inputs (e.g. proteins) for processing by CheckM
storage/	A folder with intermediate results from CheckM processing
lineage.ms	Output file describing marker set for each bin
<SAMPLE_NAME>-genes.aln	Alignment of multi-copy genes and their AAI identity
<SAMPLE_NAME>-results.txt	Final results of CheckM's lineage_wf

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 logs folder containing helpful files for you to review if the need ever arises.

Filename	Description
nf-<PROCESS_NAME>.begin	An empty file used to designate the process started
nf-<PROCESS_NAME>.err	Contains STDERR outputs from the process
nf-<PROCESS_NAME>.log	Contains both STDERR and STDOUT outputs from the process
nf-<PROCESS_NAME>.out	Contains STDOUT outputs from the process
nf-<PROCESS_NAME>.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
nf-<PROCESS_NAME>.sh	The script executed by bash for the process
nf-<PROCESS_NAME>.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 visualisation
checkm-report.html	The Nextflow Execution Report
checkm-timeline.html	The Nextflow Timeline Report
checkm-trace.txt	The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename	Description
software_versions.yml	A complete list of programs and versions used by each process
software_versions_mqc.yml	A complete list of programs and versions formatted for MultiQC

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Description	Default
--bactopia	The path to bactopia results to use as inputs

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Description	Default
--include	A text file containing sample names (one per line) to include from the analysis
--exclude	A text file containing sample names (one per line) to exclude from the analysis

CheckM Parameters

Parameter	Description	Default
--checkm_unique	Minimum number of unique phylogenetic markers required to use lineage-specific marker set.	10
--checkm_multi	Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set.	10
--aai_strain	AAI threshold used to identify strain heterogeneity	0.9
--checkm_length	Percent overlap between target and query	0.7
--full_tree	Use the full tree (requires ~40GB of memory) for determining lineage of each bin.
--skip_pseudogene_correction	Skip identification and filtering of pseudogene
--ignore_thresholds	Ignore model-specific score thresholds
--checkm_ali	Generate HMMER alignment file for each bin
--checkm_nt	Generate nucleotide gene sequences for each bin
--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
--skip_adj_correction	Do not exclude adjacent marker genes when estimating contamination

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Description	Default
--outdir	Base directory to write results to	./
--run_name	Name of the directory to hold results	bactopia
--skip_compression	Ouput files will not be compressed	False
--keep_all_files	Keeps all analysis files created	False

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter	Description	Default
--max_retry	Maximum times to retry a process before allowing it to fail.	3
--max_cpus	Maximum number of CPUs that can be requested for any single job.	4
--max_memory	Maximum amount of memory (in GB) that can be requested for any single job.	32
--max_time	Maximum amount of time (in minutes) that can be requested for any single job.	120
--max_downloads	Maximum number of samples to download at a time	3

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description	Default
--nfconfig	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_mode	Method used to save pipeline results to output directory.	copy
--infodir	Directory to keep pipeline Nextflow logs and reports.	${params.outdir}/pipeline_info
--force	Nextflow will overwrite existing output files.	False
--cleanup_workdir	After Bactopia is successfully executed, the work directory will be deleted.	False

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Description	Default
--condadir	Directory to Nextflow should use for Conda environments
--registry	Docker registry to pull containers from.	dockerhub
--singularity_cache	Directory where remote Singularity images are stored.
--singularity_pull_docker_container	Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuild	Force overwrite of existing pre-built environments.	False
--queue	Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)	general,high-memory
--cluster_opts	Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--disable_scratch	All intermediate files created on worker nodes of will be transferred to the head node.	False

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Description	Default
--monochrome_logs	Do not use coloured log outputs.
--nfdir	Print directory Nextflow has pulled Bactopia to
--sleep_time	The amount of time (seconds) Nextflow will wait after setting up datasets before execution.	5
--validate_params	Boolean whether to validate parameters against the schema at runtime	True
--help	Display help text.
--wf	Specify which workflow or Bactopia Tool to execute	bactopia
--list_wfs	List the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_params	Show all params when using --help
--help_all	An alias for --help --show_hidden_params
--version	Display version text.

Citations

If you use Bactopia and checkm 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)