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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.

bakta/
├── <SAMPLE_NAME>
│   ├── <SAMPLE_NAME>.embl
│   ├── <SAMPLE_NAME>.faa
│   ├── <SAMPLE_NAME>.ffn
│   ├── <SAMPLE_NAME>.fna
│   ├── <SAMPLE_NAME>.gbff
│   ├── <SAMPLE_NAME>.gff3
│   ├── <SAMPLE_NAME>.hypotheticals.faa
│   ├── <SAMPLE_NAME>.hypotheticals.tsv
│   ├── <SAMPLE_NAME>.tsv
│   ├── <SAMPLE_NAME>.txt
│   └── logs
│       └── bakta
│           ├── <SAMPLE_NAME>.log
│           ├── nf-bakta.{begin,err,log,out,run,sh,trace}
│           └── versions.yml
├── logs
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions.{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├── bakta-dag.dot
│   ├── bakta-report.html
│   ├── bakta-timeline.html
│   └── bakta-trace.txt
├── software_versions.yml
└── software_versions_mqc.yml

Results

Bakta

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

Extension Description
.embl Annotations & sequences in (multi) EMBL format
.faa CDS/sORF amino acid sequences as FASTA
.ffn Feature nucleotide sequences as FASTA
.fna Replicon/contig DNA sequences as FASTA
.gbff Annotations & sequences in (multi) GenBank format
.gff3 Annotations & sequences in GFF3 format
.hypotheticals.faa Hypothetical protein CDS amino acid sequences as FASTA
.hypotheticals.tsv Further information on hypothetical protein CDS as simple human readble tab separated values
.tsv Annotations as simple human readble 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 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
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 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

Bakta Parameters

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

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 bakta in your analysis, please cite the following.