ID not taken as locus tag

[nbisweden]

ID not taken as locus tag

[Juke34]

You can use the attribute of you choice as locus_tag using the --use_attribute_value_as_locus_tag parameter. But be aware that when submitting the file to ENA, the locus_tag will be anyway overwritten.

About overlapping UTR and CDS you could automatically fix it using gff3_sp_fix_features_locations_duplicated.pl from AGAT.
The same if you encounter problems with short introns you can use gff3_sp_flag_short_introns.pl .

For the gene names the easier is to have it prior conversion in the GFF file, then it will automatically be included in the EMBL file.
To load gene names from a blast output in your GFF file you can use agat_sp_manage_functional_annotation.pl.
If you want to add the gene names afterwards in the EMBL file you will have to code your own script (don't hesitate to share it then, I could include it here in case someone else would like to do the same).

[Juke34]

We didn't hear anything back from you for a while, I guess you found your way. So I close the issue but feel free to re-open it necessary.