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NCBI Prokaryotic Genome Annotation Pipeline
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[BUG] PGAP failed, docker exited with rc = 1 WARNING Final process status is permanentFail #190

Closed devikarajk closed 2 years ago

devikarajk commented 2 years ago

Describe the bug I have updated PGAP to the latest version of 2022-02-10.build5872. The test genome is working fine and I got the output. But for my genome the result is "PGAP failed, docker exited with rc = 1" and at the end its showing "WARNING Final process status is permanentFail"

Please help me to solve the issue and annotate my genome.

To Reproduce sure I am ready to share the data

Expected behavior I expected an output like I got for the test genome. I need to annotate my whole genome data

Software versions (please complete the following information):

Log Files Please rerun pgap.py with the --debug flag and attach an archive (e.g. zip or tarball) of the logs in the directory: debug/tmp-outdir/*/*.log.

Additional context I tried with --no-internet option as well, but not solved ncbiapp.log ncbiapp.log cwltool.log

azat-badretdin commented 2 years ago

Thank you for your report, Devika!

The first thing to look in cwltool.log is for the first instance of permanentFail and the error above it.

Your log says: 


line 213: ncbi::CObjectIStreamJson::UnexpectedMember() --- line 1: "publication.status": unexpected member, should be one of: "publication"  ( at JsonValue.publications.[].[])

Please verify that your input submol YAML file is correct.

For reference, please check out our documentation here: https://github.com/ncbi/pgap/wiki/Input-Files, section Metadata YAML file (submol)