<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="">If running under MPI, the only step that should take a long time would be a final clustering step (the clustering is not parallelized). It should run in well under 24 hours though, so perhaps it is a memory issue or a feature depth issue. You can try running the contig by itself and setting all the bast_depth parameters in maker_bopts.ctl to 10 to help both.<div class=""><br class=""></div><div class="">Otherwise making a large overlap for subdivided contigs (50-100kb) should be enough. Alternatively look for streches of NNNNNN’s in the contig and split on those.<br class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 22, 2017, at 9:43 AM, Seth Munholland <<a href="mailto:munholl@uwindsor.ca" class="">munholl@uwindsor.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I would think splitting could work if you generate a sufficient overlap. IE 1-100k, 50-150k, etc. Reassembling the annotations for the overlap regions may be tricky if you get conflicting annotations though.<br class=""></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class="">Seth Munholland, B.Sc.<br class=""></div><div class="">Department of Biological Sciences<br class="">
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T: <a value="+15192533000" class="">(519) 253-3000 Ext: 4755</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Thu, Jun 22, 2017 at 2:39 AM, Aravind PRASAD <span dir="ltr" class=""><<a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank" class="">aravindp@imcb.a-star.edu.sg</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div class="m_-2669857248014709785WordSection1"><p class="MsoNormal">Hi <span style="color:#1f497d" class="">All</span>,</p><div class=""> <br class="webkit-block-placeholder"></div><p class="MsoNormal">I’m trying to annotate a fish genome using Maker pipeline. It could finish the annotation for maximum scaffolds except 5 of them which are of size around 100M base pairs. The current clusters in our institute has a time limit of 24hrs for
a job and these scaffolds could not be annotated with in that time.</p><p class="MsoNormal">Can you please suggest any other way of finishing the annotation for large scaffolds?</p><div class=""> <br class="webkit-block-placeholder"></div><p class="MsoNormal">I thought of chunking up the scaffolds to run, but, I’m afraid that would split a gene into two.</p><p class="MsoNormal">Thanks for your time.</p><div class=""> <br class="webkit-block-placeholder"></div><p class="MsoNormal">Regards,</p><p class="MsoNormal"><b class=""><span style="font-size:10.0pt;font-family:"Times New Roman","serif";color:#002060" class=""><a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank" class="">Aravind PRASAD</a> :: Research Officer :: Comparative and Medical Genomics Lab :: Institue of Molecular
and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)</span></b></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Times New Roman","serif";color:#4f81bd" class="">61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID <a href="tel:+65%206586%209573" value="+6565869573" target="_blank" class="">(+65) 6586 9573</a> :: Fax <a href="tel:+65%206779%201117" value="+6567791117" target="_blank" class="">(+65) 6779 1117</a> ::
<a href="http://www.imcb.a-star.edu.sg/" target="_blank" class="">http://www.imcb.a-star.edu.sg/</a></span></p><div class=""><span class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span class=""><span id="cid:image002.png@01D2E8F3.C893C4B0"><image002.png></span>
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