Using PoGo with Stringtie GTF

[beaferbl]

Hello,
I want to use PoGo to map peptides to transcripts assembled with Stringtie and I also have a fasta with the translation of these transcripts. I am getting empty output using these files, so I guess it is something related to their structure. In my GTF I only have "transcript" and "exon" in the "type" (no "CDS") and the order of exons is different from the GENCODE format. I can modifiy them so they can follow the requirements mentioned in #13 (although I am not sure what to do with CDS information). Should it be enough?
Best regards,
Bea