Maria Jose Gomez

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Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

Yes, ``` file /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env/share/RepeatMasker/Libraries/RepeatMaskerLib.h5 /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env/share/RepeatMasker/Libraries/RepeatMaskerLib.h5: symbolic link to `Dfam.h5' ``` ``` /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env/share/RepeatMasker/famdb.py -i /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env/share/RepeatMasker/Libraries/RepeatMaskerLib.h5 info ERROR:__main__:Error reading file: [Errno 38] Unable to open file (file locking disabled on this file...

Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

Thanks! It doesn't give me that error anymore, but now it says this (which was the same problem I was having with RepeatMasker 4.1.2-p1): ``` RepeatMasker version 4.1.1 Search Engine:...

Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

The contents are: ``` Building a new DB, current time: 07/23/2021 13:47:39 New DB name: /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env2/share/RepeatMasker/Libraries/CONS-Dfam_3.3/general/is.lib New DB title: /hpcfs/home/mj.gomez12/.conda/envs/repeatmasker-env2/share/RepeatMasker/Libraries/CONS-Dfam_3.3/general/is.lib Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B...

Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

The filesystem is lustre. Running RepeatMasker locally, or in another cluster, is not an option at the moment, unfortunately.

Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

I have been trying to use the function flock, but don't quite understand how to use it, and to which files. Do you have any recommendations? Thanks again for all...

Errors from multiple programs when file locking is unavailable (e.g. "Species not known", "RepeatMasker::createLib(): Error invoking makeblastdb")

Yes.. Since this is my university's cluster, I can't do anything about it. I was able to run RepeatMasker a couple of years ago in the same cluster, but I...