PGAP error with my own data

junkim83 commented 1 year ago

Hello,

I had a problem using PGAP to analyze my own data. test genome worked, but not my data. I've attached the yaml files (changed file name extension to txt for uploading here) I used and log file I got.

Anyone help? Thanks,

cwltool.log input.txt submol.txt

azat-badretdin commented 1 year ago

Thank you for your report!

The error preceding first permanentFail in cwltool.log file is

terminate called after throwing an instance of 'ncbi::CException'
  what():  NCBI C++ Exception:
    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 Lactobacillus Plantarum

Looks like you have an organism unregistered in Taxonomy. But gettax (an NCBI command) for your input informs us that the official name is Lactiplantibacillus plantarum

Could you please replace the name with this one and try again?

Thanks

junkim83 commented 1 year ago

It works!

Thanks so much!

azat-badretdin commented 1 year ago

You are welcome!

ncbi / pgap

PGAP error with my own data #249