[maker-devel] Maker 0 genes after SNAP or with proteins.gff

[Xabier Vázquez-Campos]

Hi Ricardo,
it is likely that you are not providing enough evidences to train SNAP (or
even none at all). When you run maker2zff, the defaults may not give any
output if you don't have any EST at all. Check maker2zff -h for the
evidence filtering options to create the model. In worst case, you'll need
to run maker2zff -n which doesn't filter the evidences at all. I also
suggest to search about this on the mailing list as it has come up many
times.
Cheers,
Xabi

On Sat, 25 Apr 2020 at 02:46, Ricardo Nuno Ferreira Martins Guerreiro <
guerrer at uni-duesseldorf.de> wrote:

> Dear Makers list,
>
>
> I am struggling with Maker after many successful attempts. I don't
> understand why but my final .gff does not contain any genes, 0.
>
> I am running first an Evidence based modelling, with proteins only. Here
> I get around 40 thousand genes if I give the proteins as a fasta to
> align (if I provide a protein.gff from a previous maker try, I get 0
> genes, same problem).
>
> Afterwards I'm creating a SNAP hmm and running maker again, turning
> protein2genome=0 and snaphmm=snap.hmm as you say, but now I have 0
> genes. This happens either I keep providing proteins as a fasta or as
> .gff of a previous run.
>
> I have done this many times and it always worked. The only difference
> now is that I am using no ESTs whatsoever, only proteins. It's also
> strange that it works on the first round of maker but doesn't work on
> the SNAP rounds.
>
>
> Hope you can help,
> Ricardo_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>


-- 
Xabier Vázquez-Campos, *PhD*
*Research Associate*
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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