Error with Singularity image

[lucaskbobadilla]

Hello, I am trying to run Braker using the provided Docker image on Singularity. However, When I try the test.sh files I am getting the following error:

ERROR in file /opt/BRAKER/scripts/braker.pl at line 6008
Failed to create new species with new_species.pl, check write permissions in /opt/Augustus/config//species directory! Command was /usr/bin/perl /opt/Augustus/scripts/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/opt/Augustus/config/ 1> /dev/null 2>/home/ilm254/test3/errors/new_species.stderr

Any Ideas how to solve it?

[jayoung]

hi all,

I have the same error, also trying to get things running via singularity, trying test1.sh.

I doubt this extra piece of info is useful, but just in case, the new_species.stderr file looks like this for me:

Could not write /opt/Augustus/config/species/Sp_1/Sp_1_parameters.cfg. at /opt/Augustus/scripts/new_species.pl line 126.

Would love to know if there's a fix!

thanks,

Janet

[jayoung]

aha! I think I found the answer in an older closed issue - https://github.com/Gaius-Augustus/BRAKER/issues/609

It's working for me now.

First I used the following command to copy the /opt/Augustus/config dir to a writable place outside of the container, and to put it somewhere central for future use:

singularity exec -B $PWD:$PWD /fh/fast/malik_h/grp/malik_lab_shared/singularityImages/braker3.sif cp -R /opt/Augustus/config .
mv config /fh/fast/malik_h/grp/malik_lab_shared/singularityImages/braker3_otherFiles/augustus

I can't run the test.sh scripts as is, but I can modify each command to supply that augustus config dir, and now it runs. I made two modifications:

• with the singularity exec -B we need to bind/mount both the current working directory and the central location of the augustus config file (I chose to put that into /augustus_config inside the container)
• we add --AUGUSTUS_CONFIG_PATH=/augustus_config to the braker.pl command

The modified version of the command in test1.sh looks like this for me:

singularity exec -B $PWD:$PWD,/fh/fast/malik_h/grp/malik_lab_shared/singularityImages/braker3_otherFiles/augustus/config:/augustus_config /fh/fast/malik_h/grp/malik_lab_shared/singularityImages/braker3.sif braker.pl --AUGUSTUS_CONFIG_PATH=/augustus_config --genome=/opt/BRAKER/example/genome.fa --bam=/opt/BRAKER/example/RNAseq.bam --workingdir=test1 --GENEMARK_PATH=${ETP}/gmes --threads 8 --gm_max_intergenic 10000 --skipOptimize --busco_lineage eukaryota_odb10 &> test1.log

hope that works for you too @lucaskbobadilla

[tallnuttrbgv]

Getting similar error, but copied the config and get a new error looking for a dir that does not exit in the singularity image. See https://github.com/Gaius-Augustus/BRAKER/issues/874