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TGAC / earlham-galaxytools

Galaxy tools and workflows developed at the Earlham Institute
https://tgac.github.io/earlham-galaxytools/
MIT License
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unique constraint error #151

Open rob123king opened 2 years ago

rob123king commented 2 years ago

Having issues in galaxy doing then prep step. The annotation is unique thought so not sure why it is failing here. Is this error suggesting there are two transcripts with the same name as I don't see that in my gff?

 raise Exception(f"Error while inserting {to_insert} into transcript table: {e}")
Exception: Error while inserting ('CHILSU_01T008110-RA', None, 'cds', None, False, 'CHILSU_01G008110') into transcript table: UNIQUE constraint failed: transcript.protein_id
rob123king commented 2 years ago

Tried it for another species and get the same problem at around 8K transcripts.

nsoranzo commented 2 years ago

@rob123king Thanks for reporting the issue! In your case it seems there is a duplicated transcript protein id: cds. For a GFF3 file, the protein id of a transcript is extracted from the "CDS" lines which have this transcript as Parent. The script checks that all these CDS lines have the same ID (or Name if ID is missing) and then uses this as protein id.

Happy to have a look at your GFF3 file, if you like.

rob123king commented 2 years ago

Thanks for taking a look, I can't see the error for looking. See link of my gff. https://rrescloud.rothamsted.ac.uk/index.php/s/Y7HHVsduw5OjSIa

Best wishes Rob

On Wed, Dec 15, 2021 at 2:59 AM Nicola Soranzo @.***> wrote:

@rob123king https://github.com/rob123king Thanks for reporting the issue! In your case it seems there is a duplicated transcript protein id: cds. For a GFF3 file, the protein id of a transcript is extracted from the "CDS" lines which have this transcript as Parent. The script checks that all these CDS lines have the same ID (or Name if ID is missing) and then uses this as protein id.

Happy to have a look at your GFF3 file, if you like.

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