Prokka

Overview

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

Version 1.14.0 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is release under the GNU GPL v3 license and all usage should adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/binapps/prokka/1.14.0

A number of databases are supplied with Prokka and installed centrally. To see the list run the command:

prokka --listdb

The output is:

 Looking for databases in: /opt/apps/apps/binapps/prokka/1.14.0/db
 * Kingdoms: Archaea Bacteria Bacteria Bacteria Mitochondria Viruses
 * Genera: Enterococcus Escherichia Staphylococcus
 * HMMs: HAMAP
 * CMs: Bacteria Viruses

Running the application

Please do not run Prokka on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/binapps/prokka/1.14.0

prokka --cpus $NSLOTS arg1 arg2 ...

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission