<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>It was indeed caused by the correct_est_fusion=1 option (which is supposed to trim off UTR if it appears overlap of UTR across genes is caused by merged mRNAseq). I have attached a patch that is used to replace .../maker/lib/maker/auto_annotator.pm, and I've updated the website download to include the patch as in MAKER download version 2.31.3.</div><div><br></div><div>Thanks,</div><div>Carson</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> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Tuesday, April 1, 2014 at 9:21 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Missing UTRs in GFF<br></div><div><br></div><div dir="ltr">OK, I think I uploaded everything. I included a cleaned up version of the control file without all of my paths in case that is useful.<div><br></div><div>Thanks,</div><div>Ben</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 1, 2014 at 9:50 AM, 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"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Could upload your input fasta and hmm files as well. Sometimes I can reproduce errors using just the raw reports, but it looks like I will need the input files.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org" target="_blank">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Tuesday, April 1, 2014 at 8:38 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Missing UTRs in GFF<br></div><div><div class="h5"><div><br></div><div dir="ltr">Hi Carson,<div><br></div><div>I tried using version 2.31 on a scaffold where this problem occurred with 2.30 and got the same result, unfortunately. I did use corr_est_fusion=1 both times so this might be related. I have uploaded the sequence for this scaffold and the output directory under username "brubin". Is this the data that you meant?</div><div><br></div><div>I am also reattaching information on a representative problem gene from this scaffold that occurs at base 1330779.</div><div><br></div><div>Thanks so much for the help,</div><div>Ben</div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Mon, Mar 31, 2014 at 9:37 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div class="h5"><div>Not something I've seen before, but there was a patch for another issue that was cause by the use of avoid_est_fusion=1, that may be related. Try the current stable release 2.31, and let me know if it still happens.</div><div><br></div><div>You can also upload the contig folder from one of the regions in question here --> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" target="_blank">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div><br></div><div>Then I could verify the bug, and see if it is something that happens in the current release.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div></div></div><span><div><div class="h5"><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org" target="_blank">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Saturday, March 29, 2014 at 10:24 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Missing UTRs in GFF<br></div><div><div><div><br></div><div dir="ltr">I have annotated a eukaryotic genome with MAKER 2.30. I recently realized that there are a few genes in the GFF file produced by gff3_merge with inconsistencies in the annotated CDS and UTRs. For most of my genes, the UTRs have their own lines in the GFF file. However, for the problematic genes, the UTRs are not specified in the GFF file and all exons are annotated as CDS. The UTRs do appear in the gene header and the protein sequences are the correct length (do not include the UTR). I have attached an example from the GFF file. <div><br></div><div>Is this a known problem, or have I done something wrong? Is there an easy way to fix the GFF file? </div><div><br></div><div>Thanks for your help,</div><div>Ben<br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">_____________________________________________________<br>Benjamin ER Rubin</span><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">PhD Candidate</span><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><span style="border-collapse:separate;font-family:arial;font-size:small"><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Committee on Evolutionary Biology</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">University of Chicago</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><a href="http://benrubin.org" target="_blank"><font color="#0658b5">b</font>enrubin.org</a></span></div></span></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><br></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Division of Insects<br>
Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>USA<br>Office: <a href="tel:%28312%29%20665-7776" value="+13126657776" target="_blank">(312) 665-7776</a></span></div></div></div></div></div></div></div></div></div>
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Benjamin ER Rubin</span><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">PhD Candidate</span><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><span style="border-collapse:separate;font-family:arial;font-size:small"><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Committee on Evolutionary Biology</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">University of Chicago</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><a href="http://benrubin.org" target="_blank"><font color="#0658b5">b</font>enrubin.org</a></span></div></span></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><br></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Division of Insects<br>Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>
USA<br>Office: <a href="tel:%28312%29%20665-7776" value="+13126657776" target="_blank">(312) 665-7776</a></span></div></div></div></div></div></span></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">_____________________________________________________<br>Benjamin ER Rubin</span><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">PhD Candidate</span><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><span style="border-collapse:separate;font-family:arial;font-size:small"><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Committee on Evolutionary Biology</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">University of Chicago</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><a href="http://benrubin.org" target="_blank"><font color="#0658b5">b</font>enrubin.org</a></span></div></span></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><br></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Division of Insects<br>Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>
USA<br>Office: (312) 665-7776</span></div></div></div></div></span></body></html>