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NCBI Prokaryotic Genome Annotation Pipeline
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WARNING Final process status is permanentFail[BUG] <title> #124

Closed vappiah closed 3 years ago

vappiah commented 3 years ago

Dear Developers. Thanks for your support.

I attempted to run pgap on mydata. And had some errors displayed by pgap. I will be grateful if I can be helped to pinpoint what the issue was. Below are the error logs. pgap.log.txt pgap.log2.txt

PS. PGAP worked successfully on some of the genomes and for others it not work.

azat-badretdin commented 3 years ago

Thanks for your report, Vincent. It failed at screen_evaluate stage which indicate contamination. If you run it with -debug option the directory with results for this stage will be preserved at this step and you could view the results inside that directory.

thibaudnis commented 3 years ago

Alternatively: is there a calls.tab file in the output directory? This file contains the vector or adaptor spans that were detected by the PGAP process. If this file is present, you can either remove these spans from the assembly before trying PGAP again, or you can run on the current assembly with the flag --ignore-all-errors for PGAP to keep running despite the contamination.

azat-badretdin commented 3 years ago

Alternatively: is there a calls.tab file in the output directory?

It should be there, indeed: we do pass it all the way to the output from internal CWL calls.

vappiah commented 3 years ago

Alternatively: is there a calls.tab file in the output directory?

Hi @azat-badretdin Apologies for late response. I can confirm the calls.tab file is there. And I was able to see the adaptor sequence. Thanks for the help.

azat-badretdin commented 3 years ago

You are welcome, Vincent!