<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>Could you try version 2.31 (the current version)? I believe this is happening because you are passing in MAKER genes as pred_gff the transcripts thus ended up with the same Names and IDs as the genes being generated by the MAKER run via SNAP etc. This shouldn’t happen with model_gff, and shouldn’t happen in 2.31 (IDs and names are generated slightly differently in 2.30+).</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> Walter Eckalbar <<a href="mailto:weckalba@asu.edu">weckalba@asu.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, February 25, 2014 at 7:11 PM<br><span style="font-weight:bold">To: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</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>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] invalid gff3 format issues<br></div><div><br></div><div dir="ltr">Hi Daniel, those have been uploaded and I’m using version 2.28.<div><br></div><div>Walter</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 25 February 2014 18:02, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</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 Walter,
<div><br></div><div>Will you upload the full GFF3 and the control files that you used to this URL?</div><div><h3 style="text-align:left;color:rgb(102,102,102);font-size:1em;border-style:solid;font-family:Arial,Helvetica,sans-serif;margin:10px;border-width:1px;padding:2px 0px 2px 5px;background-image:inherit"><font color="blue"><a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=189" target="_blank">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=189</a></font></h3><div>Also, what version of MAKER are you running this with?</div></div><div><br></div><div>Thanks,</div><div>Daniel<br><div><div><br></div><div><br></div><div><br></div><div>On Feb 25, 2014, at 6:36 PM, Walter Eckalbar <<a href="mailto:weckalba@asu.edu" target="_blank">weckalba@asu.edu</a>></div><div> wrote:</div><br><blockquote type="cite"><div><div class="h5"><div dir="ltr"><div><div><div>Hi all,<br><br>
I am trying to update maker annotations with PASA and encountered errors stemming from file format issues in the gff3 file.<br><br></div>
I put a few lines from the gff3 to highlight the issue below. Basically, the problem is that there are non-unique IDs for a number of the annotations.<br><br></div>
Is there anything that can be done to right this problem? <br><br>
Thanks,<br><br></div>
Walter<br><div><br>
Lines from GFF3 file, repeated IDs are highlighted:<br><br><br>
chr1 maker gene 9377440 9432028 . - . ID=maker-chr1-pred_gff_maker-gene-4.16;Name=maker-chr1-pred_gff_maker-gene-4.16<br>
chr1 maker mRNA 9377440 9432028 . - . <span style="background-color:rgb(255,255,0)">
ID=maker-chr1-snap-gene-4.53-mRNA-1;</span>Parent=maker-chr1-pred_gff_maker-gene-4.16;Name=maker-chr1-snap-gene-4.53-mRNA-1;_AED=0.17;_eAED=0.17;_QI=66|0.88|0.82|1|1|1|28|1680|1234<br>
chr1 maker exon 9431899 9432028 . - . ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:698;Parent=maker-chr1-snap-gene-4.53-mRNA-1<br>
chr1 maker exon 9431698 9431808 . - . ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:697;Parent=maker-chr1-snap-gene-4.53-mRNA-1<br><br>
chr1 maker gene 8894975 9021577 . + . ID=maker-chr1-snap-gene-4.53;Name=maker-chr1-snap-gene-4.53<br>
chr1 maker mRNA 8894975 9021577 . + . <span style="background-color:rgb(255,255,0)"> ID=maker-chr1-snap-gene-4.53-mRNA-1;</span>Parent=maker-chr1-snap-gene-4.53;Name=maker-chr1-snap-gene-4.53-mRNA-1;_AED=0.16;_eAED=0.17;_QI=229|0.73|0.74|1|0.84|0.88|27|503|2007<br>
chr1 maker exon 8894975 8895153 . + . ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:558;Parent=maker-chr1-snap-gene-4.53-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,maker-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-snap-gene-4.53-mRNA-6,maker-chr1-snap-gene-4.53-mRNA-7,maker-chr1-snap-gene-4.53-mRNA-8,maker-chr1-snap-gene-4.53-mRNA-9,maker-chr1-snap-gene-4.53-mRNA-10,maker-chr1-snap-gene-4.53-mRNA-11<br>
chr1 maker exon 8942215 8942531 . + . ID=maker-chr1-snap-gene-4.53-mRNA-1:exon:559;Parent=maker-chr1-snap-gene-4.53-mRNA-1,maker-chr1-snap-gene-4.53-mRNA-2,maker-chr1-snap-gene-4.53-mRNA-3,maker-chr1-snap-gene-4.53-mRNA-4,maker-chr1-snap-gene-4.53-mRNA-5,maker-chr1-snap-gene-4.53-mRNA-6,maker-chr1-snap-gene-4.53-mRNA-7,maker-chr1-snap-gene-4.53-mRNA-8,maker-chr1-snap-gene-4.53-mRNA-9,maker-chr1-snap-gene-4.53-mRNA-10,maker-chr1-snap-gene-4.53-mRNA-11<br></div></div></div></div>
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