<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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>On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><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 style="">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 style=""><br></div><div style="">Regards, </div><div style="">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: 612-624-0532
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-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>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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