[maker-devel] Problem with re-annotation

[Sanea Sheikh]

Hello

I am using Maker to annotate a genome for which I only have EST data and
some protein data. I ran Maker once using this EST and protein data
(est2genome=1, protein2genome=1). I had the Maker output. I combined all
the GFF files for all the contigs. I used the combined GFF file to train
SNAP which gave me a .hmm file. Now I modified the Maker opts control file.
I provided the hmm file in snap_hmm. I set est2genome=0 and
protein2genome=0. I ran Maker again assuming that now I have trained the
gene predictor and I would have better annotations. But now the output file
that I get does not have Maker annotation. I have attached the control
files and the output file for the re-run so you can have a look and let me
know what I am doing wrong in order to re-annotate the genome using the
output from the previous run.

Sanea
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