Prokka

Introduction

Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

Versions

• 1.14.6

Commands

• prokka

• prokka-abricate_to_fasta_db

• prokka-biocyc_to_fasta_db

• prokka-build_kingdom_dbs

• prokka-cdd_to_hmm

• prokka-clusters_to_hmm

• prokka-genbank_to_fasta_db

• prokka-genpept_to_fasta_db

• prokka-hamap_to_hmm

• prokka-tigrfams_to_hmm

• prokka-uniprot_to_fasta_db

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=prokka      # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load prokka/XXXX        ### Latest version is recommended.