Prokka is a pipeline for rapidly annotating prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

References:

• T. Seeman. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014, 30:2068-2069. Pubmed  |  PMC  |  Journal

• Home page
• Manual
• Tutorial

• Module Name: prokka (see the modules page for more information)
• prokka is a multithreaded application

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=2g --cpus-per-task=4
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 ~]$
node$ module load prokka
node$ prokka --listdb
[16:11:09] Looking for databases in: /opt/anaconda/bin/../db
[16:11:09] * Kingdoms: Archaea Bacteria Mitochondria Viruses
[16:11:09] * Genera: Enterococcus Staphylococcus
[16:11:09] * HMMs: HAMAP
[16:11:09] * CMs: Bacteria Viruses
node$ cp /usr/local/apps/prokka/TEST_DATA/GCA_000021185.1_ASM2118v1_genomic.fna .
node$ prokka --cpus 4 --force \
    --kingdom Bacteria \
    --outdir prokka_GCA_000021185 \
    --genus Listeria \
    --locustag GCA_000021185 GCA_000021185.1_ASM2118v1_genomic.fna
[...snip...]

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

Create a batch input file (e.g. prokka.sh), which uses the input file 'prokka.in'. For example:

#! /bin/bash

function die {
    echo "$@" >&2
    exit 1
}

module load prokka/1.13 || die "Could not load prokka module"
cp /usr/local/apps/prokka/TEST_DATA/GCA_000021185.1_ASM2118v1_genomic.fna . \
    || die "Could not find test data"

prokka --cpus ${SLURM_CPUS_PER_TASK} --force \
    --kingdom Bacteria \
    --outdir prokka_GCA_000021185 \
    --genus Listeria \
    --locustag GCA_000021185 GCA_000021185.1_ASM2118v1_genomic.fna

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=3g --time=10 prokka.sh

This should create the following output directory:

./prokka_GCA_000021185
|-- GCA_000021185_10252016.err
|-- GCA_000021185_10252016.faa
|-- GCA_000021185_10252016.ffn
|-- GCA_000021185_10252016.fna
|-- GCA_000021185_10252016.fsa
|-- GCA_000021185_10252016.gbk
|-- GCA_000021185_10252016.gff
|-- GCA_000021185_10252016.log
|-- GCA_000021185_10252016.sqn
|-- GCA_000021185_10252016.tbl
`-- GCA_000021185_10252016.txt

Copy the example data

biowulf$ cp -r /usr/local/apps/prokka/TEST_DATA .

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

prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000008285 \
    --genus Listeria --locustag GCA_000008285 TEST_DATA/GCA_000008285.1_ASM828v1_genomic.fna
prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000021185 \
    --genus Listeria --locustag GCA_000021185 TEST_DATA/GCA_000021185.1_ASM2118v1_genomic.fna
prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000026705 \
    --genus Listeria --locustag GCA_000026705 TEST_DATA/GCA_000026705.1_ASM2670v1_genomic.fna
prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000168635 \
    --genus Listeria --locustag GCA_000168635 TEST_DATA/GCA_000168635.2_ASM16863v2_genomic.fna
prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000168815 \
    --genus Listeria --locustag GCA_000168815 TEST_DATA/GCA_000168815.1_ASM16881v1_genomic.fna
prokka --cpus ${SLURM_CPUS_PER_TASK} --force --kingdom Bacteria --outdir prokka_GCA_000196035 \
    --genus Listeria --locustag GCA_000196035 TEST_DATA/GCA_000196035.1_ASM19603v1_genomic.fna

Submit this job using the swarm command.

swarm -f prokka.swarm -g 2 -t 6 --module prokka/1.13