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Augustus on Biowulf

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

Developed by Institute for Mathematics and Computer Science at University of Greifswald

 

Example files can be copied from /usr/local/apps/augustus/example directory.

Running an interactive job

Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.


biowulf $ qsub -I -l nodes=1:g24:c16
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready

[user@pXXX]$ module load augustus
        
[user@pXXX]$ cd /data/$USER/XXXX

[user@pXXX]$ augustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff 
[user@pXXX]$ exit
qsub: job 2236960.biobos completed
user@biowulf]$ 

Submitting a single delly batch job

1. Create a script file along with the lines below. Modify the path of location before running.

2.

#!/bin/bash
# This file is runAugustus
#
#PBS -N augustus
#PBS -m be
#PBS -k oe
module load augustus
cd /data/$USER//run1
augustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff 

3. Submit the script using the 'qsub' command on Biowulf

$ qsub -l nodes=1:g24:c16 /data/$USER/runAugustus

 

Submitting a swarm of delly jobs

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). Here is a sample file:

cd /data/$USER/run1; augustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff 
cd /data/$USER/run2; augustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff
........ ........ cd /data/$USER/run20; augustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff

The '-f' and '--module' options for swarm are required

By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 -f cmdfile --module augustus

For more information regarding running swarm, see swarm.html

Documentation

http://bioinf.uni-greifswald.de/augustus/