<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="">All results are kept and placed into the final GFF3 unless you set blast_depth. Basically, most alignments are redundant and can be thrown away early in the process. But maker does not do this by default because most users tend to want to see all evidence. MAKER only uses 10 alignments to build it’s calculations anyways. The rest are just kept for reference. But the cost of keeping the other alignments around can be substantial if you are in a region with deep evidence depth (I’ve seen regions with 5,000 - 10,000 evidence alignments for some datasets). So if you set blast_depth, it tells MAKER you are ok with throwing out the extra depth early (MAKER still parses all alignments it just throws extra ones away as it determines they are not useful or are redundant). This saves a lot of time and RAM downstream at the cost of losing the alignments in the report. A depth of 10 means that no more than 10 alignments per data source will be kept per locus.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><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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