Dear IFB team,
I have been trying to use Braker2 pipline to annotate an eukaryotic genome. However I have been receiving the following error message related to Augustus:
#**********************************************************************************
# BRAKER CONFIGURATION
#**********************************************************************************
# BRAKER CALL: /shared/ifbstor1/software/miniconda/envs/braker2-2.1.4/bin/braker.pl --genome B70.soft.mask.fasta --bam B70.trans_sorted.bam --softmasking --cores 54
# Thu Sep 30 16:59:09 2021: braker.pl version 2.1.4
# Thu Sep 30 16:59:09 2021: Configuring of BRAKER for using external tools...
# Thu Sep 30 16:59:09 2021: Found environment variable $AUGUSTUS_CONFIG_PATH. Setting $AUGUSTUS_CONFIG_PATH to /shared/ifbstor1/software/miniconda/envs/augustus-3.3.3/bin/augustus
# Thu Sep 30 16:59:09 2021: ERROR: in file /shared/ifbstor1/software/miniconda/envs/braker2-2.1.4/bin/braker.pl at line 1553
AUGUSTUS_CONFIG_PATH/species (in this case /shared/ifbstor1/software/miniconda/envs/augustus-3.3.3/bin/augustus/) 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.
I tried to run with and without loading the the module of Augustus, but it does not works. As far as I understand this is due to the lack of permissions on Augustus as the c) option says. Therefore I would like to know, to use braker on the cluster Do I need to install Augustus? or it exists other way to run it?
Thank you in advance,
Jazmin