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

[Carson Holt]

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 <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_opts.ctl>_______________________________________________
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