Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file

[nbisweden]

Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file

[Juke34]

Thank you for the provided details related to your issue.
agat_sp_fix_features_locations_duplicated.pl cannot fix such case because modifying the exon will impact the underlying CDS. One solution would be to improve this script to collapse features like that to keep only one and factorize the attributes.

Submitting exon to EMBL is actually not recommanded. The information is redundant as the exon location are recoreded within the mRNA feature.
So the solution is to filter the exon during the conversion. To do so, follow the steps described here:
https://github.com/NBISweden/EMBLmyGFF3#mapping

1. run

EMBLmyGFF3 --expose_translations

2. add in translation_gff_feature_to_embl_feature.json

"exon": {
    "remove": true
}

3. run again the conversion from the same location

[rstewa03]

This worked perfectly. Thank you for your rapid response.