[maker-devel] error in snap training

[Carson Holt]

If it’s failing both ways I’m thinking this may be SNAP itself. Try these
two different versions of SNAP.

—> http://korflab.ucdavis.edu/Software/snap-2013-02-16.tar.gz
and 
—> http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz

If they both fail then contact the SNAP development group —> korflab AT
ucdavis DOT edu

Thanks,
Carson


From:  Rebecca Harris <rbharris at uw.edu>
Date:  Friday, February 28, 2014 at 1:14 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] error in snap training

Hi -

I tried this and ran cegma --genome on my original fasta file. I then tried
to use cegama2zff to convert, fathom, and forge. However, when I try to
generate new parameters with forge, I get the same error that I got when
trying to train SNAP without CEGMA: "ZOE ERROR (from forge): impossible
error5 KOG1342.20". Any suggestions would be great,
thanks!

Cheers,
Rebecca


On Tue, Feb 25, 2014 at 2:12 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Make sure you are using 2.31,  and then try the maker2zff filters
> individually.  If the protein models are not working well, use CEGMA to
> generate models. It's from the same group as SNAP.  Use cegma2zff for the
> conversion.
> 
> --Carson
> 
> Sent from my iPhone
> 
>> > On Feb 25, 2014, at 2:49 PM, Rebecca Harris <rbharris at uw.edu> wrote:
>> >
>> > Hey -
>> >
>> > I'm trying to train SNAP and am running into errors. I don't have any EST
>> evidence, just protein. My .gff file reports 10865 genes but when I run
>> maker2zff  -c0 -e0 I get back empty genome files. When I run maker2zff -n, a
>> ton of overlap_prev_exon errors get written to the screen and then with I get
>> to the forge step I get an "impossible error5". Any help would be greatly
>> appreciated.
>> >
>> > Thanks!
>> > Rebecca
>> > _______________________________________________
>> > maker-devel mailing list
>> > maker-devel at box290.bluehost.com
>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachments/20140228/e77809ff/attachment.html>