<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>What does it do?</div><div><br></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> Innocent Onsongo <<a href="mailto:onson001@umn.edu">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 12:28 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>><br><span style="font-weight:bold">Cc: </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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com">barry.utah@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: Re-annotation<br></div><div><br></div><div dir="ltr">I upgraded to 2.28 and Maker is not running. Thanks!</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, May 22, 2013 at 9:03 AM, Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</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><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="font-size:14px;font-family:Calibri,sans-serif"></div></div></div></div></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>Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">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" target="_blank">barry.utah@gmail.com</a>><br><span style="font-weight:bold">Cc: </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>Re: [maker-devel] Maker: Re-annotation<br></div><div><div class="h5"><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><div>On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:</div><br></div></div><blockquote type="cite"><div><div><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>_______________________________________________<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><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: <a href="tel:612-624-0532" value="+16126240532" target="_blank">612-624-0532</a> </div></div></div></span></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
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