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NCBI Prokaryotic Genome Annotation Pipeline
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PGAP failed, docker exited with rc = 1 #221

Closed Ahmer1122 closed 1 year ago

Ahmer1122 commented 1 year ago

Hi All,

I am facing error message (docker exited with rc=1). What baffles me is the test_genomes/MG37/input.yaml executed properly. But the error comes when I am running my data. This is the error message

PGAP version 2022-08-11.build6275 is up to date. Output will be placed in: /home/szweda/Downloads/pgap/SZA14_results.2 PGAP failed, docker exited with rc = 1 Printing log starting from failed job: cwltool.txt

Attached is the cwl log

azat-badretdin commented 1 year ago

Thank you, Ahmer, for your report!

Your log contains this:

Error: VerifySeqids: invalid seqid is used, containing non-local NCBI-style seqid: lcl|16length59293_fdepth=1.00x
Error: VerifySeqids: invalid seqid is used, containing non-local NCBI-style seqid: lcl|46length636_depth=2.15x
Error: VerifySeqids: invalid seqid is used, containing non-local NCBI-style seqid: lcl|48length400_depth=1.13x
verify-seqids: fail

this means that there is something wrong with your seqids. Try to separate lcl|16 from the rest of the FASTA header by space, and the other seqids

Ahmer1122 commented 1 year ago

Dear Azat, many thanks for your guidance.

It actually worked after I replaced the headers :)

Thanks :)

azat-badretdin commented 1 year ago

You are welcome, Ahmer! :-)