[job pgapx_yaml_ctl] completed permanentFail

Describe the bug I don't know actual problem. I ran for sometime and then just no result. i have attach the log file cwltool.log

To Reproduce

Expected behavior

Software versions (please complete the following information):

OS: ubuntu 20.04 lts
pgap.py --current
input-2021-11-29.build5742`]

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 Also when used with nohup ____ &, have error PGAP version 2021-11-29.build5742 is up to date. Output will be placed in: /mnt/e/analysis/pgap/p_a_result [Errno 17] File exists: '/mnt/e/analysis/pgap/p_a_result'

Thank you for you report.

When looking for problems, one needs to look for the first instance of permanentFail in cwltool.log. In this case it is:


[2022-01-25 05:26:10] DEBUG [job pgapx_yaml_ctl] initial work dir {}
[2022-01-25 05:26:10] INFO [job pgapx_yaml_ctl] /tmp/jak5j4ot$ pgapx_yaml_ctl \
    -ifmt \
    JSON \
    -input \
    /tmp/inx0s7c4/stg5c2fd13b-f843-4fa5-a29c-64b9440ad1d1/submol.json \
    -input-fasta \
    /tmp/inx0s7c4/stgf4bd3f30-23c2-4624-b518-891db1323766/pectobacterium_test.fasta \
    -ofmt \
    JSON \
    -output-annotation \
    input.asn \
    -output-asn-type \
    input_asn_type.txt \
    -output-ltp \
    genome.ltp.txt \
    -output-taxid \
    taxid.txt \
    -taxon-db \
    /tmp/inx0s7c4/stg00f80f2f-e4ee-412c-b9ad-8b6a48907682/taxonomy.sqlite3
terminate called after throwing an instance of 'ncbi::CSerialException'
  what():  NCBI C++ Exception:
    Error: SERIAL(CSerialException::eFormatError) "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/serial/objistr.cpp", line 1018: ncbi::CObjectIStream::ExpectedMember() --- line 1: member postal_code expected ( at JsonValue.contact_info)

As you can see there is missing information in the input: postal_code in the contact_info Could you please correct this and try again?

ncbi / pgap

[job pgapx_yaml_ctl] completed permanentFail #181