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NCBI Prokaryotic Genome Annotation Pipeline
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Error: Final process status is permanentFail #304

Closed sekhwal closed 2 months ago

sekhwal commented 2 months ago

I installed PGAP and am running it using the following command. However, I am not getting output results files and the pgap generates an error

install

./pgap.py --update

running

python3 /scripts/pgap.py -r -o P16 input_P1620800_chr.yaml

error message

WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 1 Printing log starting from failed job: ..... WARNING Final process status is permanentFail

azat-badretdin commented 2 months ago

Thank you for your report, Dr. Kumar

Could you please attach cwltool.log file?

sekhwal commented 2 months ago

cwltool.log

sekhwal commented 2 months ago

It seems installed correctly. ./pgap.py PGAP version 2024-04-27.build7426 is up to date. Please help me to figure out the issue.

azat-badretdin commented 2 months ago

Please use some species taxid in your YAML file.

azat-badretdin commented 2 months ago

This is the same issue as #303

sekhwal commented 2 months ago

Please use some species taxid in your YAML file.

I am already using 'salmonella' in submol.yaml

topology: 'circular' location: 'chromosome' organism: genus_species: 'salmonella' strain: 'P1620800_chr'

azat-badretdin commented 2 months ago

1/ Salmonella is not "species", it's "genus" 2/ We lost the functionality of supporting "genus" option in this release and we are working on restoring it soon 3/ Case might be important (usually biologists always capitalize genus in binomials, so I am not familiar with this use case).