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NAL-i5K / GFF3toolkit

Python programs for processing GFF3 files
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ValueError: max() arg is an empty sequence #117

Closed papelypluma closed 3 years ago

papelypluma commented 3 years ago

Hi GFF3toolkit developers. I'd like to seek for your help on this issue. QC part went well, but running the fix step raises a ValueError exception. For reference, I'm attaching the gff file and the error.txt here.

gff3_files.zip

Thank you.

mpoelchau commented 3 years ago

Hi @papelypluma - it looks like the models in your gff3 file are not formatted in the 'canonical' style (see https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). I'd recommend using the -noncg flag when running gff3_QC.

papelypluma commented 3 years ago

Hi @mpoelchau. Thanks for the help! I ran it with the -noncg flag then proceeded to fix without encountering any issues and errors.

mpoelchau commented 3 years ago

Great! I'll close this issue but feel free to re-open if you have more questions.