Prokka
Prokka is a software tool to annotate bacterial, archaeal and viral genomes.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu-CPU: 1.15.6
Usage
To activate the Prokka environment, run the command:
After that you can launch Prokka with the command prokka.
Prokka jobs should be run either in an interactive session or as a batch job. More information about running batch jobs can be found from the batch job section of the Roihu user guide.
You should always define the number of cores that Prokka will use with option --cpus to match the number
of cores reserved for the job. You can use the environment variable $SLURM_CPUS_PER_TASK to match the reserved
number.
For example:
Larger analyses should be executed as a batch job utilizing several cores.
A sample batch job script (batch_job_file.bash) is provided below:
#!/bin/bash
#SBATCH --job-name=prokka
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --time=24:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=16000
#SBATCH --partition=small
#SBATCH --account=your_project_name
# Set the number of threads based on cpus-per-task
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK:-1}
# Place and bind threads to single cores
# Comment the following lines if binding is not desired
export OMP_PLACES=cores
export OMP_PROC_BIND=spread
# Set up Prokka
module load 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 cores (--cpus-per-task=8) with a total of 16 GB of memory (--mem=16000).
The maximum duration of the job is 24 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 your_project_name with
the name of your project. You can use the command csc-projects to see what CSC projects you have access to.
You can submit the batch job file to the batch job system with the command:
See the Roihu user guide for more information about running batch jobs.