<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div style="word-wrap:break-word">Hi Getiria,
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<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?
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<div>On May 21, 2013, at 9:58 AM, Innocent Onsongo wrote:</div>
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<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>
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<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>
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<div>other_gff=Promoters.gff3 #promoter annotations</div>
<div>other_gff=CpG_Islands.gff3 # CpG island annotations</div>
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<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>
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<div>Regards, </div>
<div>Getiria</div>
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-- <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>
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<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>
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-- <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>
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</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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