Barrnap

Introduction

Barrnap: BAsic Rapid Ribosomal RNA Predictor.

For more information, please check its website: https://biocontainers.pro/tools/barrnap and its home page on Github.

Versions

  • 0.9.4

Commands

  • barrnap

Module

You can load the modules by:

module load biocontainers
module load barrnap

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Barrnap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=barrnap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers barrnap

barrnap --kingdom bac -o bac_16s.fasta < bac_genome.fasta > bac_16s.gff3
barrnap --kingdom euk -o euk_16s.fasta < euk_genome.fasta  > euk_16s.gff3