Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl

[mabh5]

Hello,

I see that this error shows up in the issues list quite a bit. In my case, I am running braker3 using a singularity image built and tested today using these instructions: Braker3 Install

I also downloaded the .gm_key and put it in my home directory as instructed. The key is new and so isn't expired. I checked that singularity can access the key with singularity shell:

$ srun --pty singularity shell --writable-tmpfs -B ${PWD}:${PWD} braker3.sif
srun: Account not specified in script or ~/.default_slurm_account, using latest project
To request GPUs, add --gpus-per-node X or --gpus X, where X is the desired number of GPUs.
Job 2067302 running on hopper002
Singularity> ls .gm_key
.gm_key

The command passed to the singularity image was braker.pl --genome=corrected_scaffoldsmasked.fasta --prot_seq=proteinsvert.fasta

the protein sequences were downloaded from OrthoDB as instructed.

Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes//gmes_petap.pl --verbose --seq /users/mh/braker/genome.fa --EP /users/mh/braker/genemark_hintsfile.gff --cores=1  --gc_donor 0.001 --evidence /users/mh/braker/genemark_evidence.gff  --soft_mask auto 1>/users/mh/braker/GeneMark-EP.stdout 2>/users/mh/braker/errors/GeneMark-EP.stderr
The most common problem is an expired or not present file ~/.gm_key!

Any assistance or advice would be greatly appreciated.

[kmkocot]

Providing any non-empty files from the errors directory might be helpful to the admins.

[KatharinaHoff]

Non-empty error files are always helpful, but please request help on this from the GeneMark developers via e-mail. I am not sure whether they have the issues on Github on their radar.

Kevin M. Kocot @.***> schrieb am Fr. 6. Okt. 2023 um 15:15:

Providing any non-empty files from the errors directory might be helpful to the admins.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/677#issuecomment-1750665645, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JFIWZ7VMPFBCLBSUNTX6AAAVAVCNFSM6AAAAAA5M6ZL4OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQGY3DKNRUGU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[alexlomsadze]

Hello,

First, I want to comment on reoccurring reports about the GeneMark key file. How do you ensure that the key file for GeneMark is correctly installed?

Whenever there is a concern about the key file, find the GeneMak.hmm executable and check if the GeneMark.hmm code complains about the key:

find path_to_genemark_folder  -name gmhmme3
path_to/gmhmme3 -v

In the case of the BRAKER singularity container:

singularity shell braker3.sif
find /opt  -name gmhmme3
/opt/ETP/bin/gmes/gmhmme3  -v
exit

If GeneMark.hmm complains about the key, then yes, there is a problem with it. If GeneMark.hmm complains about the missing input file with sequence, then you are set.

Alex

[alexlomsadze]

Hello,

We may start with two logfiles: /users/mh/braker/GeneMark-EP.stdout /users/mh/braker/errors/GeneMark-EP.stderr

My email is [email protected]

Another option is to open an issue at GeneMark-ETP repository https://github.com/gatech-genemark/GeneMark-ETP or we can continue here.

In any case, logfiles are a starting point.

Alex