Prokka-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.13

Author / Distributor

prokka

Description

"Prokka is a software tool for the rapid annotation of prokaryotic genomes.". More details are at prokka

Running Program

• Version 1.13, installed in /usr/local/apps/eb/prokka/1.13-foss-2016b-BioPerl-1.7.1.

To use this version of prokka, please first load the module with

ml prokka/1.13-foss-2016b-BioPerl-1.7.1

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_prokka
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=prokka.%j.out
#SBATCH --error=prokka.%j.err

cd $SLURM_SUBMIT_DIR
ml prokka/1.13-foss-2016b-BioPerl-1.7.1
prokka [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml prokka/1.13-foss-2016b-BioPerl-1.7.1 
prokka --help
Name:
  Prokka 1.13 by Torsten Seemann <torsten.seemann@gmail.com>
Synopsis:
  rapid bacterial genome annotation
Usage:
  prokka [options] <contigs.fasta>
General:
  --help            This help
  --version         Print version and exit
  --docs            Show full manual/documentation
  --citation        Print citation for referencing Prokka
  --quiet           No screen output (default OFF)
  --debug           Debug mode: keep all temporary files (default OFF)
Setup:
  --listdb          List all configured databases
  --setupdb         Index all installed databases
  --cleandb         Remove all database indices
  --depends         List all software dependencies
Outputs:
  --outdir [X]      Output folder [auto] (default '')
  --force           Force overwriting existing output folder (default OFF)
  --prefix [X]      Filename output prefix [auto] (default '')
  --addgenes        Add 'gene' features for each 'CDS' feature (default OFF)
  --addmrna         Add 'mRNA' features for each 'CDS' feature (default OFF)
  --locustag [X]    Locus tag prefix [auto] (default '')
  --increment [N]   Locus tag counter increment (default '1')
  --gffver [N]      GFF version (default '3')
  --compliant       Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)
  --centre [X]      Sequencing centre ID. (default '')
  --accver [N]      Version to put in Genbank file (default '1')
Organism details:
  --genus [X]       Genus name (default 'Genus')
  --species [X]     Species name (default 'species')
  --strain [X]      Strain name (default 'strain')
  --plasmid [X]     Plasmid name or identifier (default '')
Annotations:
  --kingdom [X]     Annotation mode:  (default 'Bacteria')
  --gcode [N]       Genetic code / Translation table (set if --kingdom is set) (default '0')
  --gram [X]        Gram: -/neg +/pos (default '')
  --usegenus        Use genus-specific BLAST databases (needs --genus) (default OFF)
  --proteins [X]    FASTA or GBK file to use as 1st priority (default '')
  --hmms [X]        Trusted HMM to first annotate from (default '')
  --metagenome      Improve gene predictions for highly fragmented genomes (default OFF)
  --rawproduct      Do not clean up /product annotation (default OFF)
  --cdsrnaolap      Allow [tr]RNA to overlap CDS (default OFF)
Computation:
  --cpus [N]        Number of CPUs to use [0=all] (default '8')
  --fast            Fast mode - only use basic BLASTP databases (default OFF)
  --noanno          For CDS just set /product="unannotated protein" (default OFF)
  --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
  --evalue [n.n]    Similarity e-value cut-off (default '1e-06')
  --rfam            Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
  --norrna          Don't run rRNA search (default OFF)
  --notrna          Don't run tRNA search (default OFF)
  --rnammer         Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)

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Installation

Source code is obtained from prokka

System

64-bit Linux