<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 Parul, Training augustus does take a long time. Much longer than for the other two predictors that you mentioned. Have you tried using the webAugustus web portal? The team that made augustus run it and can probably help you with trouble-shooting their page
for creating training sets: <a href="http://bioinf.uni-greifswald.de/webaugustus/training/create" class="">http://bioinf.uni-greifswald.de/webaugustus/training/create</a>
<div class=""><br class="">
</div>
<div class="">The error that you got regarding genemark is saying that maker can’t find the genemark and probuild executable files. These are specified in the maker_exe.ctl file, not the “opts” file. You need to put valid paths to those executable files in
for the given parameters. This is something that is usually specified during installation of MAKER. </div>
<div class=""><br class="">
</div>
<div class="">Hope that helps, </div>
<div class="">Daniel</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Nov 29, 2016, at 10:13 AM, Kudtarkar, Parul V. <<a href="mailto:parulk@caltech.edu" class="">parulk@caltech.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="auto" class="">
<div class=""><span class=""></span></div>
<div class="">
<div class=""><span class=""></span></div>
<div class=""><span class=""></span><br class="">
<span class=""></span>
<blockquote type="cite" class="">
<div id="divtagdefaultwrapper" dir="ltr" class="">
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">Dear Maker developers,</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">1. We use assembled RNAseq(from same species) and protein evidence(from evolutionary close species) to generate training gene structure(1st iteration, est2genome=1,protein2genome=1
). <br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">2. This is than used to train abinito gene predictors, SNAP and AUGUSTUS. <br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">3. GeneMarkES( version: GeneMark-ES / ET v.4.32) is used to produce training data-set with the command</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">gmes_petap.pl --sequence pmin_jelly.fa<br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">4. We would be predicting genes using results from SNAP, Genemark and AUGUSTUS(2nd iteration, est2genome=0, protein2genome=0) </span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">I have couple of questions relating to Genemark and AUGUSTUS</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">1. AUGUSTUS</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">We do not have a species file for species file of our interest or evolutionary closer species</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">following command is used to generate species file</span></font></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<div class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">/autoAug.pl --genome=pmin_jelly.fa --species=pminiata --cdna=pmin_transcripts.fa --trainingset=genome.gff3 --singleCPU -v --useexisting <br class="">
</span></font></div>
<b style="background-color: rgba(255, 255, 255, 0);" class=""><font class="">AUGUSTUS is taking too long to compute species file, is there a solution for this issue. Using species file from other organism might generate false positives. Is it advised in such
situations to not used AUGUSTUS model?</font></b>
<div class=""><br class="webkit-block-placeholder">
</div>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class=""><b class=""></b>2. Genemark<br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">I used the gmhmm file generated in the genemark output directory, however I encounter following error</span></font></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<div class="">
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">-------------------------<br class="">
</span></font></p>
<div class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class=""><b class="">STATUS: Parsing control files...<br class="">
ERROR: You have failed to provide a value for 'gmhmme3' in the control files.<br class="">
ERROR: You have failed to provide a value for 'probuild' in the control files.</b><br class="">
</span></font></div>
<font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">---------------------</span></font></div>
<font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">FYI</span></font>
<div class=""><br class="webkit-block-placeholder">
</div>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">-----<br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">maker_opts.ctl<br class="">
</span></font></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<div class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">#-----Gene Prediction<br class="">
snaphmm=/home/parul/Pmin_new/maker_snap/pmin1.hmm #SNAP HMM file<br class="">
gmhmm=/home/parul/Pmin_new/maker_snap/gmhmm.mod #GeneMark HMM file<br class="">
</span></font></div>
<div class=""><br class="webkit-block-placeholder">
</div>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">-----<br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">Using SNAP for training gene model yields over 6000-7000 additional gene. The model has good cumulative AED value. <br class="">
</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">I was hoping in addition to SNAP, if I could use AUGUSTUS and GeneMark to train the gene model to fuse dispersed models so that the gene count is within the expected
range.</span></font></p>
<p class=""><br class="">
</p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">Thanks and regards,</span></font></p>
<p class=""><font class=""><span style="background-color: rgba(255, 255, 255, 0);" class="">Parul<br class="">
</span></font></p>
</div>
</blockquote>
<div class="">
<div dir="ltr" class="">
<p class=""><br class="">
</p>
</div>
</div>
<span class="">Sent from my iPhone</span><br class="">
</div>
</div>
</div>
_______________________________________________<br class="">
maker-devel mailing list<br class="">
<a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>