funannotate: Augustus protein profile error on Mac osX

There is an error when using Augustus that seems to only show up on Mac systems. When training Augustus using BUSCO, BUSCO uses the --proteinprofile option to find a gene model that matches that protein profile. Augustus compiled on Mac throws an error here that looks like this:

augustus: ERROR
    PP::Profile: Error parsing pattern file"PF00012.13.prfl", line 9.

I’ve seen this error on several version of Augustus compiled on Mac. The error does not exist when Augustus is compiled on Linux.

The result of this is that BUSCO cannot train Augustus if running funannotate on Mac. You can still use funannotate but must pass in a valid species name using the --augustus_species parameter. The script will still run if you try to use BUSCO to train Augustus, however you will get no gene model predictions from Augusuts and only GeneMark models will get passed to EVM.

About this issue

Original URL
State: open
Created 8 years ago
Comments: 16 (9 by maintainers)

Most upvoted comments

This is still a problem on OS X only. So here is the short term fix until the Augustus developers can fix the code and/or somebody smarter than me can fix the home-brew augustus formulae.

First uninstall home-brew augustus:

brew uninstall --force augustus

Then make sure you have GCC-5 installed and bamtools:

brew install gcc5 bamtools

Now you can download the “fixed” augustus source code from my dropbox account, all I’ve changed here are some values in the Makefiles to use g++-5 and then use home-brew installed bamtools:

wget https://www.dropbox.com/s/1v3u3ii0j51faq5/augustus-3.2.1-osx.tar.gz

Unpack the code:

tar xzvf augustus-3.2.1-osx.tar.gz

Move into the directory and compile and install (might want to cross your fingers…)

#navigate
cd augustus-3.2.1

#compile
make

#install
sudo make install

Now make sure to change your AUGUSTUS_CONFIG_PATH in your ~/.bash_profile:

export AUGUSTUS_CONFIG_PATH=/opt/augustus-3.2.1/config

nextgenusfs on Sep 28, 2016