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BRAKER/GENEMARK ERROR:Can't obtain file lock: Function not implemented

I am using Braker1 for my gene predictions but running into problems with Genemark. Braker runs till it gets to the stage: NEXT STEP: execute GeneMark-ET. It then produces this error

failed to execute: perl /path/to/braker/BRAKER/gm_et_linux_64/gmes_petap/gmes_petap.pl --sequence=/path/to/braker/BRAKER/braker/guava/genome.fa --ET=/path/to/braker/BRAKER/braker/guava/hintsfile.gff  --cores=8 --soft 1000 1>/scratch/sysusers/godwin/BRAKER/Braker_qsub/braker/guava/GeneMark-ET.stdout 2>/scratch/sysusers/godwin/BRAKER/Braker_qsub/braker/guava/errors/GeneMark-ET.stderr

in the GeneMark-ET.stderr I have

Can't obtain file lock: Function not implemented

I don't know how to get around this problem. Please assist

assembly
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updated by chefer chefer • written by mafireyi • mafireyi

Did you obtain the key for gmes_petap?

The key has to be in the same directory where the program was installed.

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written by Rohit Rohit

Yes it came with the program and copied it to the home directory with

cp gm_key ~/.gm_key

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written by mafireyi • mafireyi

1 answer

Is the file system lustre?

Did you try and run the same command on a filesystem that is not lustre? I think this is can be a lustre file locking error, but it is a wild guess.

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written by chefer chefer

Hi,

Sorry for the late response. Thanks for the advice. And you were right, it was the file system, i ran braker in /tmp and it worked.

Thanks

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written by mafireyi • mafireyi

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