Augustus

Owned by Simon Alexander
Last updated: Jan 23, 2023
1 min read
1 Overview | 2 Using | 2.1.1 AUGUSTUS_CONFIG_PATH | 2.2 Multicore

Overview

  • Augustus: AUGUSTUS is a program to find genes and their structures in one or more genomes.

Using

Use the module name augustus to discover versions available and to load the application.

AUGUSTUS_CONFIG_PATH

Some augustus related commands need to write to the environment variable AUGUSTUS_CONFIG_PATH. You will not have permissions to do this into the installation folder.

[@blog1 testing]$ new_species.pl --species=bug Directory /apps/u/spack/gcc/12.2.0/augustus/3.4.0-56dwbhg/config//species is not writable. Cannot create new species. Please check whether AUGUSTUS_CONFIG_PATH is set, correctly.

If you require this, then:

# Copy the config for the installed version: For example, on Beartooth: cp -R /apps/u/spack/gcc/12.2.0/augustus/3.4.0-56dwbhg/config/ . # Then set the environment variable: export AUGUSTUS_CONFIG_PATH=/pfs/tc1/project/arcc/software/augustus/testing/config/

Re-running:

[@blog1 testing]$ new_species.pl --species=bug Will create parameters for a EUKARYOTIC species! creating directory /pfs/tc1/project/arcc/software/augustus/testing/config/species/bug/ ... creating /pfs/tc1/project/arcc/software/augustus/testing/config/species/bug/bug_parameters.cfg ... creating /pfs/tc1/project/arcc/software/augustus/testing/config/species/bug/bug_weightmatrix.txt ... creating /pfs/tc1/project/arcc/software/augustus/testing/config/species/bug/bug_metapars.cfg ... The necessary files for training bug have been created. Now, either run etraining or optimize_parameters.pl with --species=bug. etraining quickly estimates the parameters from a file with training genes. optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters. [@blog1 testing]$ ls config/species/bug/ bug_metapars.cfg bug_metapars.cgp.cfg bug_metapars.utr.cfg bug_parameters.cfg bug_weightmatrix.txt

Multicore

Some of the suite of tools can be used across multicores. Look at the help for each command to identify what it can do. For example look at optimize_augustus.pl for the --cpus option.

Please pay close attention to the output when starting commands when using multiple cores. For example: