<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Use the gmhmme3 and probuild executable bundled with the GeneMark-ES / ET v.4.29 download (not the GeneMark.hmm eukaryotic download). Also make sure you have set up the gm_key according to the install instructions for the package. You can also test out the validity of the *.mod file you are trying to run with by running gmhmme3 manually once on the command line.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 8, 2015, at 11:13 PM, Aaron McKenna <<a href="mailto:aaronmck@uw.edu" class="">aaronmck@uw.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Maker-dev list,<div class=""><br class=""></div><div class="">I've just started with the Maker2 pipeline, but I seem to be stuck at the gmhmme3 part. The install script says this is optional:</div><div class=""><br class=""></div><div class=""><div class="">**(OPTIONAL COMPONENTS)</div><div class=""><br class=""></div><div class="">1. Augustus 2.0 or higher. Download from <a href="http://bioinf.uni-greifswald.de/augustus/" class="">http://bioinf.uni-greifswald.de/augustus/</a></div><div class="">2. GeneMark-ES. Download from <a href="http://exon.biology.gatech.edu/" class="">http://exon.biology.gatech.edu</a></div></div><div class="">...</div><div class=""><br class=""></div><div class="">but if don't list a path in my exe file I get:</div><div class=""><br class=""></div><div class=""><div class="">ERROR: You have failed to provide a value for 'gmhmme3' in the control files.</div></div><div class=""><br class=""></div><div class="">If I do provide a link to the latest (GeneMark.hmm eukaryotic, version 3.48) version I get the following error a little later in the run:</div><div class=""><br class=""></div><div class=""><div class="">error in file format, /tmp/neZlIonRi_/4rlZBFukur_mod</div><div class="">ERROR: GeneMark Failed</div></div><div class=""><div class="">--> rank=NA, hostname=<a href="http://parvati.grid.gs.washington.edu/" class="">parvati.grid.gs.washington.edu</a></div><div class="">ERROR: Failed while preparing ab-inits</div><div class="">ERROR: Chunk failed at level:0, tier_type:2</div></div><div class=""><br class=""></div><div class="">Has anyone seen this before? Thanks for any info you have.</div><div class=""><br class=""></div><div class="">- Aaron</div></div>
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