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.

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── checkm
│           ├── <SAMPLE_NAME>-genes.aln
│           ├── <SAMPLE_NAME>-results.txt
│           ├── bins/
│           ├── lineage.ms
│           ├── logs
│           │   ├── checkm.log
│           │   ├── nf-checkm.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── storage/
└── bactopia-runs
    └── checkm-<TIMESTAMP>
        ├── merged-results
        │   ├── checkm.tsv
        │   └── logs
        │       └── checkm-concat
        │           ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── checkm-dag.dot
            ├── checkm-report.html
            ├── checkm-timeline.html
            └── checkm-trace.txt

Results¶

Merged Results¶

Below are results that are concatenated into a single file.

Filename	Description
checkm.tsv	A merged TSV file with `checkm` results from all samples

CheckM¶

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

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

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 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
`--bactopia`	The path to bactopia results to use as inputs Type: `string`

Filtering Parameters¶

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

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

CheckM Parameters¶

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

Optional Parameters¶

These optional parameters can be useful in certain settings.

Parameter	Description
`--outdir`	Base directory to write results to Type: `string`, Default: `./`
`--run_name`	Name of the directory to hold results Type: `string`, Default: `bactopia`
`--skip_compression`	Ouput files will not be compressed Type: `boolean`
`--datasets`	The path to cache datasets to Type: `string`
`--keep_all_files`	Keeps all analysis files created Type: `boolean`

Max Job Request Parameters¶

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

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

Nextflow Configuration Parameters¶

Parameters to fine-tune your Nextflow setup.

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

Nextflow Profile Parameters¶