<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
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="color: rgb(102, 102, 102); font-size: 1em; margin: 10px; padding: 2px 0px 2px 5px; background-image: inherit; background-size: inherit; background-attachment: inherit; background-origin: inherit; background-clip: inherit; background-color: rgb(255, 255, 255); font-family: Arial, Helvetica, sans-serif; text-align: left; border-style: solid; border-width: 1px; position: static; z-index: auto; ">
<font color="blue"><a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=189">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">weckalba@asu.edu</a>></div>
<div> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<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>
_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br>
</blockquote>
</div>
<br>
</div>
</body>
</html>