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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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error: GeneMark-ETP/rnaseq/gmst not writable #593

Open panosioannidis opened 1 year ago

panosioannidis commented 1 year ago

BRAKER3 fails to execute with the following message:

ERROR in file /home/panos/Programs/BRAKER/scripts/braker.pl at line 5474
Failed to execute: /usr/bin/perl /home/panos/Programs/GeneMark-ETP/bin/gmetp.pl --cfg /data/braker_1/braker/GeneMark-ETP/etp_config.yaml --workdir /data/braker_1/braker/GeneMark-ETP --bam /data/braker_1/braker/GeneMark-ETP/etp_data/ --cores 12 --softmask  1>/data/braker_1/braker/errors/GeneMark-ETP.stdout 2>/data/braker_1/braker/errors/GeneMark-ETP.stderr
Failed to execute: /usr/bin/perl /home/panos/Programs/GeneMark-ETP/bin/gmetp.pl --cfg /data/braker_1/braker/GeneMark-ETP/etp_config.yaml --workdir /data/braker_1/braker/GeneMark-ETP --bam /data/braker_1/braker/GeneMark-ETP/etp_data/ --cores 12 --softmask  1>/data/braker_1/braker/errors/GeneMark-ETP.stdout 2>/data/braker_1/braker/errors/GeneMark-ETP.stderr
The most common problem is an expired or not present file ~/.gm_key!

However, I do have a valid ~/.gm_key, so this is not a problem.

The contents of /data/braker_1/braker/errors/GeneMark-ETP.stdout are much more informative:

error: , /data/braker_1/braker/GeneMark-ETP/rnaseq/gmst not writable

My workdir is on an NFS and files are created by the users user (not my user), so I guess that this could be causing the problems. I changed the permissions for the above gmst directory to 777 (it was 755) and re-ran the command that failed to execute, and everything worked fine this time! However, it won't run the full pipeline.

So, do you have any idea why only this command has a problem with permissions? Because looking at the braker/GeneMark-ETP/ directory I can see that other directories were created successfully and contain data... Is there a specific problem with gmst?

Thank you in advance.

PS: I have the same problem, both with the singularity image, as well as the manually installed version of BRAKER.

KatharinaHoff commented 1 year ago

@MarioStanke This is an ETP issue.