search

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
Other
307 stars 90 forks source link

Failure to complete annotation #199

Closed bharat1912 closed 2 years ago

bharat1912 commented 2 years ago

Hi, Thank you for the WGS annotation tool. I have installed and run the example data (MG37) with only one issue "WARNING: open files is less than the recommended value of 8000" though the annotation went to completion.

I had some problems relating to structure of the YAML file, the sequence fasta file, out of memory etc. I had looked through the log file to correct the issues. However, I am not sure where the problem lies with the current error noted in the log file which is attached.

cwltool.log

Thanks in advance for looking into the issue.

azat-badretdin commented 2 years ago

This part of the cwltool.log is relevant:


    Error: SERIAL(CSerialException::eFormatError) "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/serial/objistrjson.cpp", line 213: ncbi::CObjectIStreamJson::UnexpectedMember() --- line 1: "location": unexpected member, should be one of: "strain" "genus_species"  ( at JsonValue.organism.genus_species)

Looks like there is a formatting problem in your submol.yaml file. The line location: got probably misidented.