<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>If it’s failing both ways I’m thinking this may be SNAP itself. Try these two different versions of SNAP. </div><div><br></div><div>—> <a href="http://korflab.ucdavis.edu/Software/snap-2013-02-16.tar.gz">http://korflab.ucdavis.edu/Software/snap-2013-02-16.tar.gz</a></div><div>and </div><div>—> <a href="http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz">http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz</a></div><div><br></div><div>If they both fail then contact the SNAP development group —> korflab AT ucdavis DOT edu</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Rebecca Harris <<a href="mailto:rbharris@uw.edu">rbharris@uw.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, February 28, 2014 at 1:14 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] error in snap training<br></div><div><br></div><div dir="ltr">Hi -<div><br></div><div>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,</div><div>thanks!</div><div><br></div><div>Cheers,</div><div>Rebecca</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Feb 25, 2014 at 2:12 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br><br>
--Carson<br><br>
Sent from my iPhone<br><div><div class="h5"><br>
> On Feb 25, 2014, at 2:49 PM, Rebecca Harris <<a href="mailto:rbharris@uw.edu">rbharris@uw.edu</a>> wrote:<br>
><br>
> Hey -<br>
><br>
> 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.<br>
><br>
> Thanks!<br>
> Rebecca<br></div></div>> _______________________________________________<br>
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