Centrally installed Braker2 error: AUGUSTUS_CONFIG_PATH/species is not writeable.

Question

[Timotheus]

Hi,

I'm trying to run Braker2 to annotate my genome with the help of RNA-seq data:

 braker.pl \
  --genome=$ASSEMBLY \
  --bam=$RNA_BAM \
  --gff3 \
  --cores=$THREADS

I get an error:

# Fri Aug 12 18:07:33 2022: ERROR: in file /apps/system/easybuild/software/BRAKER/2.1.6-foss-2019b-Python-3.7.4/scripts/braker.pl at line 1710
AUGUSTUS_CONFIG_PATH/species (in this case /apps/system/easybuild/software/AUGUSTUS/3.3.3-foss-2019b/config/) is not writeable.
There are 3 alternative ways to set this variable for braker.pl:
   a) provide command-line argument --AUGUSTUS_CONFIG_PATH=/your/path
   b) use an existing environment variable $AUGUSTUS_CONFIG_PATH
      for setting the environment variable, run
           export AUGUSTUS_CONFIG_PATH=/your/path
      in your shell. You may append this to your .bashrc or
      .profile file in order to make the variable available to all
      your bash sessions.
   c) braker.pl can try guessing the location of
      $AUGUSTUS_CONFIG_PATH from an augustus executable that is
      available in your $PATH variable.
      If you try to rely on this option, you can check by typing
           which augustus
      in your shell, whether there is an augustus executable in
      your $PATH
      Be aware: the $AUGUSTUS_CONFIG_PATH must be writable for
                braker.pl because braker.pl is a pipeline that
                optimizes parameters that reside in that
                directory. This might be problematic in case you
                are using a system-wide installed augustus
                installation that resides in a directory that is
                not writable to you as a user.

Braker2 was kindly installed by someone managing our cluster on my request, but this means I will not have write permissions for the Augustus config. I myself failed with a conda installation of Braker2. Any way to overcome this error with the central installation?

Thanks for any suggestions!

Answer 1

[Michael]

How about trying mentioned options a) or b), e.g.in the cluster submission script add the following:

### CLUSTER CONFIG, Load modules, etc.

export AUGUSTUS_CONFIG_PATH=$HOME/augustus_config_path
mkdir -p $AUGUSTUS_CONFIG_PATH
### Run BRAKER
braker.pl ....

[Timotheus]

But how would I get the Augustus config file to reside under this path if Braker is centrally installed? This doesn't work, I tried similar solutions previously, apologies for not mentioning...

[Michael]

Sorry, I haven't tried this myself because I don't have a running braker pipeline myself yet. There are two possibilities, either Braker generates the config file on the fly, then changing the path should work. If it requires an existing config file there to start from, I would try to copy everything over from the global path. like so:

cp -r /apps/system/easybuild/software/AUGUSTUS/3.3.3-foss-2019b/config/ $AUGUSTUS_CONFIG_PATH

If that doesn't work either you should ask the braker developers.