Bactopia Tool - `gtdb`¶

The gtdb tool uses GTDB-Tk's classify workflow to assign taxonomic classifications to your set of samples. This is done through the use of the Genome Taxonomy Database. If you are unsure of your sequences, gtdb is useful tool to help determine the taxonomy of your samples.

Example Usage¶

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

Output Overview¶

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

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── gtdb
│           ├── align
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.filtered.tsv
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.msa.fasta.gz
│           │   └── <SAMPLE_NAME>.{ar122|bac120}.user_msa.fasta.gz
│           ├── classify
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.classify.tree.1.tree
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.classify.tree.6.tree
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.summary.tsv
│           │   ├── <SAMPLE_NAME>.{ar122|bac120}.tree.mapping.tsv
│           │   └── <SAMPLE_NAME>.backbone.{ar122|bac120}.classify.tree
│           ├── gtdbtk.json
│           ├── identify
│           │   ├── <SAMPLE_NAME>.ar53.markers_summary.tsv
│           │   ├── <SAMPLE_NAME>.bac120.markers_summary.tsv
│           │   ├── <SAMPLE_NAME>.failed_genomes.tsv
│           │   └── <SAMPLE_NAME>.translation_table_summary.tsv
│           ├── logs
│           │   ├── nf-gtdb.{begin,err,log,out,run,sh,trace}
│           │   ├── results
│           │   │   ├── gtdbtk.log
│           │   │   └── gtdbtk.warnings.log
│           │   └── versions.yml
│           └── <SAMPLE_NAME>.{ar122|bac120}.summary.tsv
└── bactopia-runs
    └── gtdb-<TIMESTAMP>
        ├── merged-results
        │   ├── gtdb.tsv
        │   └── logs
        │       └── gtdb-concat
        │           ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── gtdb-dag.dot
            ├── gtdb-report.html
            ├── gtdb-timeline.html
            └── gtdb-trace.txt

Results¶

GTDB-Tk¶

Below is a description of the per-sample results from GTDB-Tk. For full details about each of the GTDB output files, see GTDB-Tk Classify Workflow page.

Filename	Description
<SAMPLE_NAME>.{ar122	bac120}.classify.tree
<SAMPLE_NAME>.{ar122	bac120}.filtered.tsv
<SAMPLE_NAME>.{ar122	bac120}.markers_summary.tsv
<SAMPLE_NAME>.{ar122	bac120}.msa.fasta
<SAMPLE_NAME>.{ar122	bac120}.summary.tsv
<SAMPLE_NAME>.{ar122	bac120}.user_msa.fasta
<SAMPLE_NAME>.translation_table_summary.tsv	Summary of the translation table used for each genome
<SAMPLE_NAME>.ar122.markers_summary.tsv	Summary of unique, duplicated, and missing markers within the 122 archaeal marker set for each submitted genome
<SAMPLE_NAME>.bac120.markers_summary.tsv	Summary of unique, duplicated, and missing markers within the 120 bacterial marker set for each submitted genome

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
gtdb-dag.dot	The Nextflow DAG visualisation
gtdb-report.html	The Nextflow Execution Report
gtdb-timeline.html	The Nextflow Timeline Report
gtdb-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`

GTDB Setup Parameters¶

Parameter	Description
`--gtdb`	Tarball or path of a GTDB database. If a database is not found, you must use '--download_gtdb' Type: `string`
`--download_gtdb`	Download the latest GTDB database, even it exists Type: `boolean`
`--gtdb_save_as_tarball`	Download the latest GTDB database, and save it in a single tarball Type: `boolean`
`--skip_check`	Do not check the installation of GTDB database Type: `boolean`

GTDB Classify Parameters¶

Parameter	Description
`--min_af`	Minimum alignment fraction to consider closest genome Type: `number`, Default: `0.65`
`--min_perc_aa`	Filter genomes with an insufficient percentage of AA in the MSA Type: `integer`, Default: `10`
`--gtdb_tmp`	Specify alternative directory for temporary files Type: `boolean`, Default: `/tmp`
`--gtdb_use_scratch`	Reduce pplacer memory usage by writing to --gtdb_tmp location (slower) Type: `boolean`
`--gtdb_debug`	Create intermediate files for debugging purposes Type: `boolean`
`--force_gtdb`	Continue processing if an error occurs on a single genome 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¶