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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Yunxi,
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<div>During the maker installation, there is an option to automatically install MPICH2, which would let you run maker parallelized. Try rerunning the perl Build.PL script in the "maker/src" directory, and when the option to install MPICH2 comes up, tell it
yes. This will start an automated download and install onto your server.</div>
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<div>You can also start more than one maker process. They will work on annotating the genome together. You can start as many as ten or more processes like this, but MPI is a better parallelizing option. </div>
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<div>Hope that helps,</div>
<div>Daniel</div>
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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div id="divRpF353708" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel [maker-devel-bounces@yandell-lab.org] on behalf of Yunxi Lin [lin11@cougars.csusm.edu]<br>
<b>Sent:</b> Monday, June 24, 2013 5:11 PM<br>
<b>To:</b> Carson Holt<br>
<b>Cc:</b> maker-devel@yandell-lab.org; Amelia Ireland<br>
<b>Subject:</b> Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
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<div style="">Thank your for your help. </div>
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<div style="">My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs
from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER. </div>
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<div style="">I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus. </div>
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<div style="">Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way. </div>
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<div style="">Sincerely,</div>
<div style="">Yunxi</div>
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<div class="gmail_quote">2013/6/24 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br>
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<div>Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use. If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time. This is especially true if you use the
alt_est option for evidence as these are aligned via tblastx which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.</div>
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<div>Also you do not need results from the entire genome to train SNAP. If you get results from ~10Mb of the genome that is usually sufficient. Also make sure you are taking advantage of parallelization. Launch via MPI to get maximum performance. I commonly
launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Amelia Ireland <<a href="mailto:amelia.ireland@gmod.org" target="_blank">amelia.ireland@gmod.org</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, 23 June, 2013 10:15 PM<br>
<span style="font-weight:bold">To: </span><<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Cc: </span><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Subject: </span>[maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">From the GMOD helpdesk; please cc Lin, <a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>.<br>
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<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Yunxi Lin</b> <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
Date: Sun, Jun 23, 2013 at 4:14 PM<br>
Subject: about running MAKER<br>
To: "<a href="mailto:gmod-help@gmod.org" target="_blank">gmod-help@gmod.org</a>" <<a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>><br>
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<div dir="ltr"><span style="font-size:14px; font-family:arial,sans-serif">Hi </span>
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<div style="font-family:arial,sans-serif; font-size:14px">I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for
the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server. </div>
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<div style="font-family:arial,sans-serif; font-size:14px">Thank you. </div>
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<div style="font-family:arial,sans-serif; font-size:14px">Sincerely,</div>
<div style="font-family:arial,sans-serif; font-size:14px">Lin</div>
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-- <br>
<div dir="ltr">Amelia Ireland<br>
GMOD Community Support
<div><a href="http://gmod.org" target="_blank">http://gmod.org</a> || @gmodproject
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