Maker 0 genes after SNAP or with proteins.gff

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Maker 0 genes after SNAP or with proteins.gff

Ricardo Guerreiro
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
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Re: 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 <[hidden email]> 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
[hidden email]
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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Re: Maker 0 genes after SNAP or with proteins.gff

Carson Holt-2
In reply to this post by Ricardo Guerreiro
You would have to look at the alignments, but I suspect they do not align in a way to the gene models to supply sufficient support for the annotation. If it is the maker2zff script producing 0 genes, that it because it requires at least some EST evidence. You can change that using the command line options.

—Carson

> On Apr 24, 2020, at 8:27 AM, Ricardo Nuno Ferreira Martins Guerreiro <[hidden email]> 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_opts.ctl>_______________________________________________
> maker-devel mailing list
> [hidden email]
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org