ERROR-convert_ensembl : the gene_id for ? is associated to multiple chromosomes(Pp05, Pp04). Use non ambiguous gene ids (e.g ensembl ids) please.

[15132522078]

When I convert a normal GTF file to an Ensemble format GTF file, I get the above error. But I am sure that there is no such thing as gene_id duplication. Are there any other potential errors that may cause the above error?

[dputhier]

Hello,
It's hard to say without having the file. Could you provide me with the GTF file so that I can check ?
Best

[dputhier]

Note that it aso could be related to a format issue as the gene_id is "?". This would mean that some elements have no gene_ids.

[15132522078]

Thank you very much for your reply. I think I've solved this problem. There are some exon comment lines(Shown below) in my gtf file that do not contain gene_id. After removing these exon comment lines, i can convert it to a GTF file in Ensemble format.
Pp04 maker exon 297331 297502 . - . transcript_id "PpG0000003482.01.T01"; Pp04 maker exon 1178790 1179481 . - . transcript_id "PpG0000003305.01.T01"; Pp04 maker exon 2438500 2438536 . - . transcript_id "PpG0000002963.01.T01"; Pp04 maker exon 2438667 2438883 . - . transcript_id "PpG0000002963.01.T01"; Pp04 maker exon 2439007 2439112 . - . transcript_id "PpG0000002963.01.T01"; Pp04 maker exon 3006626 3007046 . - . transcript_id "PpG0000002928.01.T03"; Pp04 maker exon 3123882 3125305 . + . transcript_id "PpG0000002826.01.T04"; Pp04 maker exon 3124379 3125305 . + . transcript_id "PpG0000002826.01.T01"; Pp04 maker exon 3292873 3293880 . - . transcript_id "PpG0000002802.01.T02"; Pp04 maker exon 3293992 3294147 . - . transcript_id "PpG0000002802.01.T01";