AUGUSTUS

Overview

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

Version 2.7 (pre-compiled binaries) is installed on the CSF.

Restrictions on use

AUGUSTUS is open source under Artistic License 2.0

Set up procedure

To access the software you must load the AUGUSTUS modulefile first:

module load apps/binapps/augustus/2.7

This modulefile sets the variable AUGUSTUS_CONFIG_PATH to the config directory in the install location.

Running the application

Please do not run AUGUSTUS on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

• Make sure you have the modulefile loaded
• Create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
### The above uses the current directory where you should have all relevant files
#$ -V
### The above inherits your user environment from the login node i.e. so it can find commands

augustus --genemodel=complete --outfile=outfile.gff3 --species=aspergillus_fumigatus sequence_file.fa

• Submit: qsub scriptname

Parallel batch job submission

Augustus cannot currently run on more than one core on the CSF.

Further info

• AUGUSTUS website
• README file containing information on how to use the software
• Tutorial