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

[Gowthaman Ramasamy]

Carson,
I also tried to use maker's genemart_gtf2gff script to create valid gff3 file. I seem to have problems with it too.
Here is what I see...

-bash-3.2$ ~/software/maker/bin/genemark_gtf2gff3 CrfA_v13.3.5_supercontigs.gff2
ERROR: Cannot understand format
expecting -> gene_id "xxxx"; transcript_id "xxxx";

Attached is first 10000 lines of the GTF output from genemark.

Any help/pointers will be really appreciated.

Thanks again,
Gowthaman
________________________________________
From: Gowthaman Ramasamy
Sent: Wednesday, June 06, 2012 6:53 PM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: GFF3 file format not accepted by pred_gff options

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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