Skip to content



Prokka is a software tool to annotate bacterial, archaeal and viral genomes.


Free to use and open source under GNU GPLv3.


Prokka 1.14.6 is Available in Puhti.


In Puhti, Prokka should be executed as a batch job. An interactive batch job for testing Prokka can be started with command:

sinteractive -i -m 8G

Prokka is installed to Puhti as a bioconda environment called prokka. In addition to Prokka, this environment contains also Roary pan genome pipeline. To use it, you should activate Prokka environment with commands:

export PROJAPPL=/projappl/your_project_name
module load bioconda
source activate prokka

After that you can launch Prokka with command prokka. By default Prokka tries to use 8 coputing cores, but in this interactive batch job case, you have just one core available. Because of that you should always define the number of cores that Prokka will use with option -cpus.

For example:

prokka  --cpus 1 contigs.fasta

Larger analysis should be executed as a batch job utilizing several cores. Sample batch job script (batch_job_file.bash) below.

#!/bin/bash -l
#SBATCH --job-name=prokka
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --time=24:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1  
#SBATCH --cpus-per-task=8
#SBATCH --mem=16000
#SBATCH --account=your_project_name

#set up prokka
export PROJAPPL=/projappl/your_project_name
module load bioconda
source activate prokka

#Run prokka
prokka --cpus $SLURM_CPUS_PER_TASK --outdir results_case1 --prefix mygenome contigs_case1.fa

In the batch job example above one Prokka task (--ntasks 1) is executed. The job reserves 8 core (--cpus-per-task=8 ) with total of 16 GB of memory (--mem=16000). The maximum duration of the job is twelve hours (--time 24:00:00 ). All the cores are assigned from one computing node (--nodes=1 ). In addition to the resource reservations, you have to define the billing project for your batch job. This is done by replacing the your_project_name with the name of your project. (You can use command csc-workspaces to see what projects you have in Puhti).

You can submit the batch job file to the batch job system with command:

sbatch batch_job_file.bash

See the Puhti user guide for more information about running batch jobs.

More information

Last edited Mon Mar 29 2021