Centrally installed Braker2 error: AUGUSTUS_CONFIG_PATH/species is not writeable.
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Entering edit mode
7 weeks ago
Timotheus ▴ 20

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
.profile file in order to make the variable available to all
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!

braker2 augustus • 449 views
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Entering edit mode
7 weeks ago

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 ....

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Entering edit mode

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...

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Entering edit mode

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.