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Bakta prokaryote annotation software setup and use

GETTING STARTED

Bakta is a genome annotation "wrapper" for prokaryotes and plasmids that outperforms other software, such as Prokka, in annotation comprehensitivity and applying functional annotations.

You will need a prokaryote genome assembly to proceed. If you are using the Ohio Super Computer (OSC) and have access to PAS1568, skip installation to OSC USE.




INSTALLING

Pull the Bakta Container

Use Singularity (or Docker) to pull the Bakta container.

singularity pull docker://quay.io/biocontainers/bakta:latest

Install databases.

<CONTAINER.sif>
bakta_db download --output <DB_DIRECTORY>

Continue to OSC USE.




OSC USE

Keep it clean (create a directory)

It is best practice to create a directory for a particular analysis. I personally prefer to create a directory for every genome annotation, e.g.:

mkdir <OUTPUT_DIR>/<GENOME_CODENAME>/bakta

Preparing Bakta commands

For high performance computing environments, such as OSC, it is necessary to create TWO scripts: 1 script will call on Bakta to run the annotation command, while another script will invoke Singularity, the container software, to call Bakta.

Bakta script

Create a .sh script file in UTF-8 using a plain-text editor. Copy and fill in the following commands' arguments (<>) with your genome's metadata, and omit --gram if unknown. There are several notes to consider:

  • If your genome is a plasmid, then append --plasmid <PLASMID_NAME>
  • If your genome is complete (to chromosome/plasmid level), then append --complete
  • If your genome is a metagenoome, then append --meta
bakta --db /fs/ess/PAS1568/databases/bakta/ --genus <GENUS> \
--species <SPECIES> --gram <+/-/?> --strain <STRAIN> -t 8 \
-o <YOUR/OUTPUT/DIRECTORY> <YOUR/ASSEMBLY/PATH>

Once complete, save your script as a .sh file, such as bakta.sh, then transfer it to a folder in OSC.

Singularity job script

The Singularity job script will call on the script you just wrote to launch the job on the high performance computing environment. For the SLURM job scheduler, which OSC uses, create another UTF-8 formatted file using a plain-text editor; make sure the path <YOUR/BAKTA_SCRIPT.sh> references the OSC path of the script you previously made above:

#!/bin/bash
#SBATCH --job-name=<YOUR_JOB_NAME>
#SBATCH --output=<YOUR_JOB_NAME>
#SBATCH --error=<YOUR_JOB_NAME>
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH -A PAS1568

singularity exec /fs/ess/PAS1568/software/bakta/bakta.sif /bin/bash <YOUR/BAKTA_SCRIPT.sh>

Once complete, save your script as a .sh file, such as bakta_execution.sh, then transfer it to a folder in OSC.


Executing Bakta command

sbatch <bakta_execution.sh>



CITATION INFO

Bakta is the wrapper that packages many other software. In addition to citing Bakta, you should cite the included software, such as Prodigal, Aragorn, tRNAScan, Infernal, Rfam, Blast, Diamond, Hmmer, Pfam, etc, depending on the software used in your analysis.