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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Hi All,
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">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></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Carson, Can you please explain what exactly does the blast_depth option does while running Maker?</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Thank you all for your time!</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Regards,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Aravind.</span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt; font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt; font-family:"Tahoma","sans-serif""> Carson Holt [mailto:carsonhh@gmail.com]
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<b>Sent:</b> Friday, 23 June, 2017 12:06 PM<br>
<b>To:</b> Seth Munholland<br>
<b>Cc:</b> Aravind PRASAD; maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Maker annotation of large scaffolds</span></p>
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<p class="MsoNormal">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.</p>
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<p class="MsoNormal">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.</p>
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<p class="MsoNormal">—Carson</p>
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<p class="MsoNormal">On Jun 22, 2017, at 9:43 AM, Seth Munholland <<a href="mailto:munholl@uwindsor.ca">munholl@uwindsor.ca</a>> wrote:</p>
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<p class="MsoNormal">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.</p>
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<p class="MsoNormal">Seth Munholland, B.Sc.</p>
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<p class="MsoNormal">Department of Biological Sciences<br>
Rm. 304 Biology Building<br>
University of Windsor<br>
401 Sunset Ave. N9B 3P4<br>
T: (519) 253-3000 Ext: 4755</p>
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<p class="MsoNormal">On Thu, Jun 22, 2017 at 2:39 AM, Aravind PRASAD <<a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank">aravindp@imcb.a-star.edu.sg</a>> wrote:</p>
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<p class="MsoNormal" style="">Hi <span style="color:#1F497D">All</span>,</p>
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<p class="MsoNormal" style="">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" style="">Can you please suggest any other way of finishing the annotation for large scaffolds?</p>
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<p class="MsoNormal" style="">I thought of chunking up the scaffolds to run, but, I’m afraid that would split a gene into two.</p>
<p class="MsoNormal" style="">Thanks for your time.</p>
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<p class="MsoNormal" style="">Regards,</p>
<p class="MsoNormal" style=""><b><span style="font-size:10.0pt; color:#002060"><a href="mailto:aravindp@imcb.a-star.edu.sg" target="_blank">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" style=""><span style="font-size:9.0pt; color:#4F81BD">61 Biopolis Drive :: #5-04 Proteos :: Singapore 138673:: DID
<a href="tel:+65%206586%209573" target="_blank">(+65) 6586 9573</a> :: Fax <a href="tel:+65%206779%201117" target="_blank">
(+65) 6779 1117</a> :: <a href="http://www.imcb.a-star.edu.sg/" target="_blank">http://www.imcb.a-star.edu.sg/</a></span></p>
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