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¶