<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="">You need to install augustus and place the species parameter files into the …/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <<a href="mailto:willett4@email.unc.edu" class="">willett4@email.unc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hi All-
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<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>
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<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>
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<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>
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<span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:Contig149</span></div>
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<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>
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<div class="">Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?</div>
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<div class="">Thanks for any help you can give me,</div>
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<div class="">Best,</div>
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<div class="">Chris Willett</div>
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<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>
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