unique constraint error

[rob123king]

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]

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

[nsoranzo]

@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]

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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#151 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBMFHOGGKFV2AN3IQGH4F3URAAA7ANCNFSM5KBHGFTQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.