[maker-devel] Problem with re-annotation

[Carson Holt]

Hi Sanea,

There are no snap calls in your results.  It’s as if SNAP never even ran.
Did you capture STDERR from your second run?  If so can you send it to me.
I just want to see if it even shows SNAP as having run in the progress
reports. 

Thanks,
Carson

From:  Sanea Sheikh <saneasheikh at gmail.com>
Date:  Monday, January 13, 2014 at 2:17 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Problem with re-annotation

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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