<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="">Also you can run MPI within a single node and not across nodes. This will still give a performance bonus equal to the MPI process count<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 23, 2017, at 2:25 AM, Aravind PRASAD <<a href="mailto:aravindp@imcb.a-star.edu.sg" class="">aravindp@imcb.a-star.edu.sg</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi All,</span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you for your inputs. Currently, I’m not using the MPI version but running Maker in multiple instances. Previously, I tried to run the MPI version but failed. Though the installation had no issues with MPI-Maker.</span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Carson, Can you please explain what exactly does the blast_depth option does while running Maker?</span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you all for your time!</span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Regards,</span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Aravind.</span></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></p><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><b class=""><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>Carson Holt [<a href="mailto:carsonhh@gmail.com" style="color: purple; text-decoration: underline;" class="">mailto:carsonhh@gmail.com</a>]<span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, 23 June, 2017 12:06 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Seth Munholland<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>Aravind PRASAD;<span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;" class="">maker-devel@yandell-lab.org</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Maker annotation of large scaffolds</span></div></div></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" 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><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" 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.</div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">—Carson</div></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p><div class=""><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Jun 22, 2017, at 9:43 AM, Seth Munholland <<a href="mailto:munholl@uwindsor.ca" style="color: purple; text-decoration: underline;" class="">munholl@uwindsor.ca</a>> wrote:</div></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" 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.</div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br clear="all" class=""></div><div class=""><div class=""><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Seth Munholland, B.Sc.</div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Department of Biological Sciences<br class="">Rm. 304 Biology Building<br class="">University of Windsor<br class="">401 Sunset Ave. N9B 3P4<br class="">T: (519) 253-3000 Ext: 4755</div></div></div></div></div><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Thu, Jun 22, 2017 at 2:39 AM, Aravind PRASAD <<a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank" style="color: purple; text-decoration: underline;" class="">aravindp@imcb.a-star.edu.sg</a>> wrote:</div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Hi<span class="Apple-converted-space"> </span><span style="color: rgb(31, 73, 125);" class="">All</span>,</div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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.</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Can you please suggest any other way of finishing the annotation for large scaffolds?</div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">I thought of chunking up the scaffolds to run, but, I’m afraid that would split a gene into two.</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Thanks for your time.</div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Regards,</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><b class=""><span style="font-size: 10pt; color: rgb(0, 32, 96);" class=""><a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank" style="color: purple; text-decoration: underline;" class="">Aravind PRASAD</a><span class="Apple-converted-space"> </span>:: Research Officer :: Comparative and Medical Genomics Lab :: Institue of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)</span></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 9pt; color: rgb(79, 129, 189);" class="">61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID<span class="Apple-converted-space"> </span><a href="tel:+65%206586%209573" target="_blank" style="color: purple; text-decoration: underline;" class="">(+65) 6586 9573</a><span class="Apple-converted-space"> </span>:: Fax<span class="Apple-converted-space"> </span><a href="tel:+65%206779%201117" target="_blank" style="color: purple; text-decoration: underline;" class="">(+65) 6779 1117</a><span class="Apple-converted-space"> </span>::<span class="Apple-converted-space"> </span><a href="http://www.imcb.a-star.edu.sg/" target="_blank" style="color: purple; text-decoration: underline;" class="">http://www.imcb.a-star.edu.sg/</a></span></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><image002.png> <span class="Apple-converted-space"> </span></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"> </p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br class=""><span style="font-size: 7.5pt; font-family: Arial, sans-serif; color: gray;" class=""><br class="">Note: This message may contain confidential information. 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