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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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failed to execute miniprothint.py #31

Closed COMInterop closed 11 months ago

COMInterop commented 1 year ago

Hello,

This may be a continuation of https://github.com/Gaius-Augustus/GALBA/issues/20.

I am running the Docker container on a Mac. The program terminates with the following error:

[Sat Apr 22 04:41:12 2023] error: exited due to an error in command: grep stop_codon /Volumes/data/annotate/galba/miniprot.gff | grep proteinEnd=1 > /Volumes/data/annotate/galba/tmp/stopsAllEndcbot99o4.gff ERROR in file /opt/GALBA/scripts/galba.pl at line 3345 failed to execute: /opt/miniprothint/miniprothint.py /Volumes/data/annotate/galba/miniprot.gff --workdir /Volumes/data/annotate/galba --ignoreCoverage!

I see you asked the previous poster to 'share a couple of proteins that produce this error'. How can I know which ones are problematic?

Thank you!

tomasbruna commented 1 year ago

Hi @paracontias,

if you can upload your whole input somewhere, I'd take a look. No need to hunt for individual sequences.

Tomas

COMInterop commented 1 year ago

I just emailed it to you

KatharinaHoff commented 11 months ago

I assume that this issue was resolved a while ago.

tomasbruna commented 11 months ago

Yes resolved. I think this was caused by using input proteins with stops in them (a '*' in the line ends). This was fixed in https://github.com/tomasbruna/miniprot-boundary-scorer/commit/a4c3ab1222e8351f1c39c5776e576d45e2ca2529