<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</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>
<div>
<div>Are you using MAKER version 2.10? I ask because there is in issue with other_gff in that version that has since been fixed. So if you don't get other_gff to pass-through, you will need to upgrade to 2.28 (release date is later today coincidentally).</div>
<div><br>
</div>
<div>For the Augustus GFF3 file, the format is a little weird which is causing the problem. They are mRNA features not attached to genes. Rather than build the expected 3 level gene/mRNA/exon structure for these, it is simpler just to convert it to the 2
level match/match_part structure. Just convert the 'mRNA' tag to 'match' and all 'exon' tags to 'match_part'. Rename the GFF3 when your done so that it will force rebuild of the GFF3 database when you run again.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px; ">
</div>
</div>
</div>
</div>
</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>Innocent Onsongo <<a href="mailto:onson001@umn.edu">onson001@umn.edu</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, 22 May, 2013 8:47 AM<br>
<span style="font-weight:bold">To: </span>Barry Moore <<a href="mailto:barry.utah@gmail.com">barry.utah@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span><<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] Maker: Re-annotation<br>
</div>
<div><br>
</div>
<div dir="ltr">No. The MAKER produced GFF3 file does not contain any annotations. I even tried setting the keep_preds parameter to 1 (keep_preds=1) to see if it will pass annotations from the Augustus produced GFF file into the final annotation but that didn't
work. I have attached the <span style="font-size: 13px; font-family: arial, sans-serif; ">maker_opts.ctl file I used together with the first 100 lines of the GFF files it's using. I also include the GFF file produced by MAKER (</span><span style="background-color: rgb(245, 245, 245); font-size: 13px; font-weight: bold; white-space: nowrap; font-family: arial, sans-serif; ">CGS01058First100.gff)</span>
<div><span style="font-size: 13px; font-family: arial, sans-serif; "><br>
</span></div>
<div><span style="font-size: 13px; font-family: arial, sans-serif; "><br>
</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, May 21, 2013 at 10:43 PM, Barry Moore <span dir="ltr">
<<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@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="word-wrap:break-word">Hi Getiria,
<div><br>
</div>
<div>Does the MAKER produced GFF3 file contain any annotations at all? Can you send the first ~100 lines each of the MAKER produced GFF3 file and of the GFF3 files that you passed via maker_opts.ctl?
<div><br>
</div>
<div>B</div>
<div><br>
<div>
<div>
<div class="h5">
<div>On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">Maker Development Team,
<div><br>
</div>
<div>I am trying to use Maker for re-annotation using gene predictions from Augustus. We had previously used Augustus for gene prediction but now want to combine these annotations with some EST data. I updated fields maker_opts.ctl as below</div>
<div><br>
</div>
<div>genome=CGS01058.fasta #genome sequence file in fasta format</div>
<div>est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT</div>
<div>pred_gff=Augustus.gff3 #ab-initio predictions from<br>
</div>
<div>
<div>other_gff=Promoters.gff3 #promoter annotations</div>
<div>other_gff=CpG_Islands.gff3 # CpG island annotations</div>
</div>
<div><br>
</div>
<div>Maker runs to completion and according to the log file annotation was successful. However, it also gives a "Segmentation fault (core dumped)" message. It does produce a GFF3 file but when I load the GFF3 file into IGV and look it does not contain any of
the exon definitions in Augustus.gff3. Am I missing something? </div>
<div><br>
</div>
<div>Regards, </div>
<div>Getiria</div>
<div>
<div><br>
</div>
-- <br>
Getiria Onsongo, Ph.D.<br>
Informatics Analyst, Research Informatics Support System<br>
Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>
Minneapolis, MN 55455<br>
Phone: <a href="tel:612-624-0532" value="+16126240532" target="_blank">612-624-0532</a></div>
</div>
</div>
</div>
<div class="im">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br>
</div>
</blockquote>
</div>
<span class="HOEnZb"><font color="#888888"><br>
<div><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px">
<div><span style="font-family:Arial;font-size:12px">
<div>Barry Moore</div>
<div>Research Scientist</div>
<div>Dept. of Human Genetics</div>
<div>University of Utah</div>
<div>Salt Lake City, UT 84112</div>
<div>--------------------------------------------</div>
<div><a href="tel:%28801%29%20585-3543" value="+18015853543" target="_blank">(801) 585-3543</a></div>
<div><br>
</div>
</span></div>
<div><br>
</div>
</span><br>
</div>
<br>
</font></span></div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Getiria Onsongo, Ph.D.<br>
Informatics Analyst, Research Informatics Support System<br>
Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>
Minneapolis, MN 55455<br>
Phone: 612-624-0532 </div>
</span>
</body>
</html>