Bactopia Tool - `bakta`¶

The bakta module uses Bakta to rapidly annotate bacterial genomes and plasmids in a standardized fashion. Bakta makes use of a large database (40+ GB) to provide extensive annotations including: tRNA, tmRNA, rRNA, ncRNA, CRISPR, CDS, and sORFs.

Example Usage¶

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

Output Overview¶

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

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── main
│       └── annotator
│           └── bakta
│               ├── <SAMPLE_NAME>-blastdb.tar.gz
│               ├── <SAMPLE_NAME>.embl.gz
│               ├── <SAMPLE_NAME>.faa.gz
│               ├── <SAMPLE_NAME>.ffn.gz
│               ├── <SAMPLE_NAME>.fna.gz
│               ├── <SAMPLE_NAME>.gbff.gz
│               ├── <SAMPLE_NAME>.gff3.gz
│               ├── <SAMPLE_NAME>.hypotheticals.faa.gz
│               ├── <SAMPLE_NAME>.hypotheticals.tsv
│               ├── <SAMPLE_NAME>.tsv
│               ├── <SAMPLE_NAME>.txt
│               └── logs
│                   ├── nf-bakta.{begin,err,log,out,run,sh,trace}
│                   └── versions.yml
└── bactopia-runs
    └── bakta-<TIMESTAMP>
        └── nf-reports
            ├── bakta-dag.dot
            ├── bakta-report.html
            ├── bakta-timeline.html
            └── bakta-trace.txt

Results¶

Bakta¶

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

Extension	Description
.blastdb.tar.gz	A gzipped tar archive of BLAST+ database of the contigs, genes, and proteins
.embl.gz	Annotations & sequences in (multi) EMBL format
.faa.gz	CDS/sORF amino acid sequences as FASTA
.ffn.gz	Feature nucleotide sequences as FASTA
.fna.gz	Replicon/contig DNA sequences as FASTA
.gbff.gz	Annotations & sequences in (multi) GenBank format
.gff3.gz	Annotations & sequences in GFF3 format
.hypotheticals.faa.gz	Hypothetical protein CDS amino acid sequences as FASTA
.hypotheticals.tsv	Further information on hypothetical protein CDS as simple human readable tab separated values
.tsv	Annotations as simple human readable tab separated values
.txt	Broad summary of `Bakta` annotations

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

Bakta Download Parameters¶

Parameter	Description
`--bakta_db`	Tarball or path to the Bakta database Type: `string`
`--bakta_db_type`	Which Bakta DB to download 'full' (~30GB) or 'light' (~2GB) Type: `string`, Default: `full`
`--bakta_save_as_tarball`	Save the Bakta database as a tarball Type: `boolean`
`--download_bakta`	Download the Bakta database to the path given by --bakta_db Type: `boolean`

Bakta Parameters¶

Parameter	Description
`--proteins`	FASTA file of trusted proteins to first annotate from Type: `string`
`--prodigal_tf`	Training file to use for Prodigal Type: `string`
`--replicons`	Replicon information table (tsv/csv) Type: `string`
`--min_contig_length`	Minimum contig size to annotate Type: `integer`, Default: `1`
`--keep_contig_headers`	Keep original contig headers Type: `boolean`
`--compliant`	Force Genbank/ENA/DDJB compliance Type: `boolean`
`--skip_trna`	Skip tRNA detection & annotation Type: `boolean`
`--skip_tmrna`	Skip tmRNA detection & annotation Type: `boolean`
`--skip_rrna`	Skip rRNA detection & annotation Type: `boolean`
`--skip_ncrna`	Skip ncRNA detection & annotation Type: `boolean`
`--skip_ncrna_region`	Skip ncRNA region detection & annotation Type: `boolean`
`--skip_crispr`	Skip CRISPR array detection & annotation Type: `boolean`
`--skip_cds`	Skip CDS detection & annotation Type: `boolean`
`--skip_sorf`	Skip sORF detection & annotation Type: `boolean`
`--skip_gap`	Skip gap detection & annotation Type: `boolean`
`--skip_ori`	Skip oriC/oriT detection & annotation Type: `boolean`
`--bakta_opts`	Extra Backa options in quotes. Example: '--gram +' Type: `string`

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¶