Bakta is a tool for the rapid standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON bioinformatics standard file formats for automated downstream analysis.

References:

• Schwengers O. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11)..

• bakta Main Site

• Module Name: bakta (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • bakta_HOME
• Example files in ???
• Reference data in /fdb/bakta/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load bakta

[user@cn3144 ~]$ bakta
usage: bakta [--db DB] [--min-contig-length MIN_CONTIG_LENGTH] [--prefix PREFIX] [--output OUTPUT] [--force] [--genus GENUS]
             [--species SPECIES] [--strain STRAIN] [--plasmid PLASMID] [--complete] [--prodigal-tf PRODIGAL_TF]
             [--translation-table {11,4}] [--gram {+,-,?}] [--locus LOCUS] [--locus-tag LOCUS_TAG] [--keep-contig-headers]
             [--compliant] [--replicons REPLICONS] [--regions REGIONS] [--proteins PROTEINS] [--meta] [--skip-trna] [--skip-tmrna]
             [--skip-rrna] [--skip-ncrna] [--skip-ncrna-region] [--skip-crispr] [--skip-cds] [--skip-pseudo] [--skip-sorf]
             [--skip-gap] [--skip-ori] [--skip-plot] [--help] [--verbose] [--debug] [--threads THREADS] [--tmp-dir TMP_DIR]
             [--version]
             
bakta: error: the following arguments are required:  

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. bakta.sh). For example:

#!/bin/bash
set -e
module load bakta
bakta < bakta.in > bakta.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] bakta.sh

Create a swarmfile (e.g. bakta.swarm). For example:

bakta < bakta.in > bakta.out
bakta < bakta.in > bakta.out
bakta < bakta.in > bakta.out
bakta < bakta.in > bakta.out

Submit this job using the swarm command.

swarm -f bakta.swarm [-g #] [-t #] --module bakta