prokka on Biowulf
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
Documentation
Important Notes
- Module Name: prokka (see the modules page for more information)
- prokka is a multithreaded application
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
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 ~]$
Batch job
Most jobs should be run as batch jobs.
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 ${SLURM_CPUS_PER_TASK} --force \ --kingdom Bacteria \ --outdir prokka_GCA_000021185 \ --genus Listeria \ --locustag GCA_000021185 GCA_000021185.1_ASM2118v1_genomic.fna
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=6 --mem=3g --time=10 prokka.sh
This should create the following output directory:
./prokka_GCA_000021185 |-- GCA_000021185_10252016.err |-- GCA_000021185_10252016.faa |-- GCA_000021185_10252016.ffn |-- GCA_000021185_10252016.fna |-- GCA_000021185_10252016.fsa |-- GCA_000021185_10252016.gbk |-- GCA_000021185_10252016.gff |-- GCA_000021185_10252016.log |-- GCA_000021185_10252016.sqn |-- GCA_000021185_10252016.tbl `-- GCA_000021185_10252016.txt
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Copy the example data
biowulf$ 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/1.13where
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module prokka | Loads the prokka module for each subjob in the swarm |