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Gabaldonlab / perSVade

perSVade: personalized Structural Variation detection
GNU General Public License v3.0
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Issue with the repeat_inference #15

Closed guidopuccetti closed 1 year ago

guidopuccetti commented 1 year ago

Dear Miquel,

I am having an issue with the mounting point, which I previously did not encounter and I would like your opinion.

Currently this is the script I am running sbatch -c 16 --wrap="docker run -v /data4/guido/perSVade:/reference_genome_dir -v /data4/guido/perSVade:/output_directory mikischikora/persvade:v1.02.6 python -u ./scripts/perSVade infer_repeats -o /output_directory/repeat_inference -r /reference_genome_dir/reference_genome.fasta --fraction_available_mem 0.20"

The error I get is the following but unfortunately is not really informative

### SLURM JOB STATS ########################
#
#
### SLURM JOB OUTPUT ########################
Running module infer_repeats...
ERROR conda.cli.main_run:execute(34): Subprocess for 'conda run ['python', '-u', './scripts/perSVade', 'infer_repeats', '-o', '/output_directory/repeat_inference', '-r', '/reference_genome_dir/reference_genome.fasta', '-thr', '16', '--fraction_available_mem', '0.20']' command failed.  (See above for error)

Since I am still not yet really familiar with Docker, I am really curious to hear from you! Thanks!

MikiSchikora commented 1 year ago

Hi,

If I understand correctly, you are mounting the folder /data4/guido/perSVade of the host into two different folders inside the container /output_directory and /reference_genome_dir right? This may be the source of the problem, and it could be solved by mounting once. For instance:

docker run -v /data4/guido/perSVade:/perSVade_run mikischikora/persvade:v1.02.6 python -u ./scripts/perSVade infer_repeats -o /perSVade_run/repeat_inference -r /perSVade_run/reference_genome.fasta --fraction_available_mem 0.20

Does this make sense? I'd recommend testing this outside of slurm running, just as a single command to verify that the pipeline starts. If the problem persists, could you send me the full log?

Best,

Miquel Àngel Schikora

PS: I see that such commands may be confusing, and we are working on an easier wrapper for future versions, that automatically handles mounting and docker/singularity runs. However, this is still a work in progress.

MikiSchikora commented 1 year ago

Good morning,

Is this solved? I'd close the issue if so.

Best, Miquel Àngel Schikora