[maker-devel] GFF3 file format not accepted by pred_gff options

[Gowthaman Ramasamy]

Hi Carson,
As I wrote to you earlier, I was able to successfully create a gff3 file from our predictor to be used in pred_gff option. But, now, I am trying to add another abinitio prediction (GeneMark-prokaryotic).  For some weird reasons,  I would like to run GeneMark-prokaryote and Augustus-eukaryotes. So, i am not able to run both inside maker.

But, that gff3 was not used by pred_gff. I tried to make it as similar to the working gffs as possible. Still in vein. Would you mind having look at the attached gff file. I even run it by gff validator at modencode(http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online). All passed.

In the maker produced gff i just see one pair of match-matchpart that corresponds to entire supercontig from GeneMark. Not corresponding to genes.

I really appreciate your time and help. 

Gowthaman

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