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NCBI Prokaryotic Genome Annotation Pipeline
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PGAP failed, docker exited with rc = 1 #222

Closed JuanAranguiz closed 2 years ago

JuanAranguiz commented 2 years ago

Hello! First of all, thanks for PGAP. I've tried to run my file and no matter how hard I try I can't. If anyone could advise me I would really appreciate it. PGAP_failed.zip

azat-badretdin commented 2 years ago

Than you for your report, @JuanAranguiz !

The file you sent says: 

    Error: CWL(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/app/cloud/cwl/pgapx_yaml_ctl.cpp", line 246: CPgapxYamlCtlApplication::Run() --- Unknown organism Arthrobacter sp

Notice the missing dot in the end. Please add a dot to the organism line in submol YAML input and try again

JuanAranguiz commented 2 years ago

Thank you for your response and kindness. I don't understand where I should write the dot. I attach my submol YAML input file and if you could clarify me I would appreciate it

topology: 'linear' location: 'chromosome' organism: genus_species: 'Arthrobacter sp.'

azat-badretdin commented 2 years ago

Thanks! You already have the dot. Hmmm... We will have a look!

azat-badretdin commented 2 years ago

Just to confirm: you are using latest, August, release, correct?

JuanAranguiz commented 2 years ago

I downloaded PGAP with this command curl -OL https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py I really don't know what version it is I'm sorry for the doubts, I really don't know much about the area

azat-badretdin commented 2 years ago

If you downloaded that recently, then it is the latest version

azat-badretdin commented 2 years ago

I opened an internal ticket (see Label) and we will address this issue, hopefully in the current process of releasing September version of PGAPx.

Cheers!

azat-badretdin commented 2 years ago

@JuanAranguiz I failed to reproduce this failure locally using as an input FASTA one of our Arthrobacter sp assemblies.

Could you please send me an example of the FASTA header you used as an input? (the lines that start with >)