GFF Error: overlapping duplicate nucleic_acid feature

[minor7b5]

I have ran the following:

gffread my.gff3 -T -o my.gtf

The output file is empty and I get a long list of errors such as:

GFF Error: overlapping duplicate polypeptide feature (ID=pep_L.tenue_CDS|Contig_168610|L.tenue_CDS|Contig_168610_119_196_r) GFF Error: overlapping duplicate nucleic_acid feature (ID=L.tenue_CDS|Contig_168983)

Could you please advise on how to overcome this issue?

Thanks