Biowulf High Performance Computing at the NIH
Augustus on Biowulf
AUGUSTUS is a gene prediction program written by Mario Stanke, Oliver Keller, Stefanie K├Ânig, Lizzy Gerischer and Katharina Hoff. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS can also predict the genes simultaneously in several aligned genomes (see README-cgp.txt).

Documentation

https://github.com/Gaius-Augustus/Augustus

Important Notes
Submitting an interactive job

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive --mem=10g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load augustus

[cn0135]$ cp -rp /usr/local/apps/augustus/version/examples/example.fa /data/$USER
[cn0135]$ augustus --species=human example.fa


[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

Submitting a single batch job

1. Create a script file (myscript) similar to the one below

#! /bin/bash
# myscript
set -e

module load augustus || exit 1
cd /data/$USER/
augustus --species=human example.fa

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g myscript

Using Swarm

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; augustus species=human example.fa
cd /data/$USER/dir2; augustus species=human example.fa
cd /data/$USER/dir3; augustus species=human example.fa
...
cd /data/$USER/dir20; augustus species=human example.fa

submit the swarm job:

$ swarm -f cmdfile --module augustus -g 5

For more information regarding running swarm, see swarm.html