BRAKER via Singularity working directory, config path issues

[emgiles]

I have been running BRAKER via singularity. The .sif file and gene mark key are located in /home/user. I can successfully run BRAKER if I copy my genome.fasta and my protein_seq.faa to my /home/user directory, but I have not been able to run the program 1.) by specifying a different working directory path or 2.) by specifying the path to the .sif file. How to solve?? My home directory cannot handle the size of the files created.

1.) Error when trying to run the program from outside of /home/user (--workingdir=/full_path/work_subdir): Use of uninitialized value $workDir in -d at /opt/BRAKER/scripts/braker.pl line 811. Use of uninitialized value $workDir in concatenation (.) or string at /opt/BRAKER/scripts/braker.pl line 812. Use of uninitialized value $workDir in mkdir at /opt/BRAKER/scripts/braker.pl line 814. Use of uninitialized value $workDir in concatenation (.) or string at /opt/BRAKER/scripts/braker.pl line 814. ERROR: in file /opt/BRAKER/scripts/braker.pl at line 815

2.) Error when trying to specify path to .sif and running from outside my working directory: (singularity exec /home/user/braker3.sif braker.pl --species=Gen_sp --genome=genome.fasta --prot_seq=protseq.faa --softmasking --workingdir=name_subdir --threads=15 --GENEMARK_PATH=/home/user) WARNING: in file /opt/BRAKER/scripts/braker.pl at line 1893 AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config//species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location. cp: cannot create directory '/home/user/.augustus': No such file or directory

Advice???

[splaisan]

HI @emgiles, not 100% sure it answers your question but I just ran the singularity using additional -B arguments that allow you to specify other paths like workingdir.

here is my script

# .sif files are stored in SIFFILES
SIFFILES=/opt/sif_files
thr=24

singularity exec \
  -B ${PWD}:/data \
  -B ${ORTHODB}:/orthodb \
  ${SIFFILES}/braker3.sif braker.pl \
  --species="artificial_inteligence" \
  --genome="/data/AI.fa" \
  --prot_seq="/orthodb/Vertebrata.fa" \
  --workingdir="/data/braker_out" \
  --threads="${thr}"

[emgiles]

Thanks Stephane

I am going to try this! Previously I have just run from my home directory which has worked but no idea for space requirements. Cheers Emily

On Mon, May 8, 2023 at 10:18 AM Stephane Plaisance @.***> wrote:

HI @emgiles https://github.com/emgiles, not 100% sure it answers your question but I just ran the singularity using additional -B arguments that allow you to specify other paths like workingdir.

here is my script

.sif files are stored in SIFFILES

SIFFILES=/opt/sif_files thr=24

singularity exec \ -B ${PWD}:/data \ -B ${ORTHODB}:/orthodb \ ${SIFFILES}/braker3.sif braker.pl \ --species="artificial_inteligence" \ --genome="/data/AI.fa" \ --prot_seq="/orthodb/Vertebrata.fa" \ --workingdir="/data/braker_out" \ --threads="${thr}"

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[jowodo]

609 and #610 might be related.

[KatharinaHoff]

The files that BRAKER will copy to your home directory are relatively small. That won't be the main job output files, BRAKER is only copying the config folder of Augustus. Did you try additionally mounting your home directory to the singularity run?

[emgiles]

Hi, Yes probably mounting the home directory to singularity would work. In the end I just ran in the home directory which worked fine.