Purdue University

Commands

• prokka
• prokka-abricate_to_fasta_db
• prokka-biocyc_to_fasta_db
• prokka-build_kingdom_dbs
• prokka-cdd_to_hmm
• prokka-clusters_to_hmm
• prokka-genbank_to_fasta_db
• prokka-genpept_to_fasta_db
• prokka-hamap_to_hmm
• prokka-tigrfams_to_hmm
• prokka-uniprot_to_fasta_db

Module

You can load the modules by:

module load biocontainers
module load prokka 

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run prokka on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=prokka
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers prokka

prokka --compliant --centre UoN --outdir PRJEB12345 --locustag EHEC --prefix EHEC-Chr1 contigs.fa  --cpus 24
prokka-genbank_to_fasta_db Coccus1.gbk Coccus2.gbk Coccus3.gbk Coccus4.gbk > Coccus.faa