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NCBI Prokaryotic Genome Annotation Pipeline
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no results #231

Closed kdyoung100 closed 1 year ago

kdyoung100 commented 1 year ago

PGAP version 2022-10-03.build6384 is up to date.

commend ./pgap.py -r -o result /data1/tools/pgap/test_genomes-2022-10-03.build6384/MG37/input.yaml

i don't know error

please tell me how to fix the error

cwltool.log

azat-badretdin commented 1 year ago

Thank you, user @kdyoung100 for your report, this is an unfortunate problem related to a third party operations problem, which we are going to fix in the next release. For now the workaround is to remove "publications:" line from submol.yaml input file for your example.

This issue is a duplicate of #230

azat-badretdin commented 1 year ago

For now the workaround is to remove "publications:" line from submol.yaml input file for your example.

I have added a somewhat simpler workaround option by modifying, temporarily, out test case to eliminate aforementioned publications: section, so you can, if you want, wipe out existing installation and reinstall PGAPx with new test data....