<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi All-
<div class=""><br class="">
</div>
<div class="">I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That
seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn’t seem to be working. Is
this the best way to do this? It looks like we don’t currently have Augustus installed on our server where I am running these programs. </div>
<div class=""><br class="">
</div>
<div class="">The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "<font face="Menlo" class=""><span style="font-size: 11px;" class="">ERROR: Non-unique top level ID”, "BLAST engine
error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence”, and this chunk:</span></font></div>
<div class=""><br class="">
</div>
<div class="">"<span style="font-family: Menlo; font-size: 11px;" class="">ERROR: Failed while prepare section files</span></div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Chunk failed at level:12, tier_type:3</span></div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:Contig149</span></div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; min-height: 13px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Chunk failed at level:4, tier_type:0</span></div>
<div class=""><span style="font-family: Menlo; font-size: 11px;" class="">FAILED CONTIG:Contig149</span><font face="Menlo" class=""><span style="font-size: 11px;" class="">”</span></font></div>
<div class=""><br class="">
</div>
<div class=""> </div>
<div class="">Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?</div>
<div class=""><br class="">
</div>
<div class="">Thanks for any help you can give me,</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Chris Willett</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br class="">
Research Associate Professor<br class="">
Department of Biology<br class="">
CB#3280 Coker Hall<br class="">
University of North Carolina, Chapel Hill<br class="">
Chapel Hill, NC, 27599-3280 <br class="">
<br class="">
Office: Genome Sciences Building 2252<br class="">
phone:<span class="Apple-tab-span" style="white-space: pre;"> </span>919-843-8663<br class="">
fax:<span class="Apple-tab-span" style="white-space: pre;"> </span>919-962-1625<br class="">
<br class="">
<a href="http://labs.bio.unc.edu/Willett/" class="">http://labs.bio.unc.edu/Willett/</a></div>
</div>
</div>
</div>
<br class="">
</body>
</html>