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<div>If the log is growing then it is still working. The time it takes is a function of the evidence dataset, genome size, and gene density. Is there any way, you could try starting a second maker process in the same directory with additional CPUs to get
it to complete sooner (each process will detect each other and avoid overlapping on their work, so it will still get divided up efficiently). Also if you combine the length of all finished contigs, you will get a better idea of how much run time is remaining
(i.e. See if contigs remaining are short or long compared to most contigs in the assembly).</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 23, 2013 1:12 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; ">Thanks Carson,</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
</span></div>
<span style="font-family: Calibri, sans-serif; font-size: 14px; ">gephy.transcripts.fa is 64406072</span><br>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; ">geph_AS_masked.fa is 296693827</span><span style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; ">The log is growing. It finished 21700 scaffolds. I think we have nearly 38149 scaffolds. Is that means the program running good? </span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; ">Sincerely,</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; ">Yunxi</span></div>
<div><span style="font-family: Calibri, sans-serif; font-size: 14px; "><br>
</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/22 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Nothing looks out of the ordinary. How big is this file --> gephy.transcripts.fa</div>
<div>How big is this file --> geph_AS_masked.fa</div>
<div><br>
</div>
<div>Also is the STDERR log growing or is it frozen?</div>
<div><br>
</div>
<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, July 22, 2013 12:24 PM
<div>
<div class="h5"><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
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<div>Sorry to bother you again. I ran the MAKER for like around two weeks, but it is still running now. I attached my control files. Can you help me to see if I set something wrong? I used the masked genome as my input, so I skipped the repeatmasker in maker.
I think it should be faster. I ran this mpiexec -n 8 maker</div>
<div><br>
</div>
<div>I'm running another maker using unmasked data in 16 threads, so I ran this in 8. I already got 34G data for this. Because the time cost in running already out of schedule. I'm worry about something wrong in the setting.</div>
<div><br>
</div>
<div>Thank you. </div>
<div>Yunxi</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/14 Yunxi Lin <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thank you Carson.</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/14 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>I would use the same data to train both.</div>
<div><br>
</div>
<div>More information here --> <a href="https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J" target="_blank">https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J</a></div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
</div>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Friday, July 12, 2013 9:04 PM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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</div>
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<div><br>
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<div>
<div dir="ltr">One more is when I train the SNAP and Augustus, should I do them in the same time with the est2genome and protein2genome, or do them separately? Thank you.</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/12 Yunxi Lin <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Carson
<div><br>
</div>
<div>The MAKER is running fine right now. I'm confusing about using the CEGMA with MAKER to train the SNAP and Augustus.</div>
<div><br>
</div>
<div>I'm running the MAKER from est2genome with protein2genome without using the result from CEGMA. I think the data I already enough for generating the hmm. </div>
<div><br>
</div>
<div>And I got the zff from the result of CEGMA, and I followed the link last time you gave me to generate the file for SNAP and Augustus.</div>
<div><br>
</div>
<div>I'm not that clear how to combine the hmm model from CEGMA and MAKER. </div>
<div><br>
</div>
<div>Thank you for your help.</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Yunxi</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Yunxi Lin <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thank you Carson. I think I should better to use the default, in case it occurs an error after several days' running.</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Some operations are not NFS safe (NFS behaves different than normal file systems). So maker performs those operations in the temporary directory. If you redirect those files to an NFS location, you may get errors (basically MAKER just dies). It won't
necessarily happen, but the warning lets you know that, if it fails then you should set TMP= somewhere else before trying again.</div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
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<div><br>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 3:22 PM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
<div><br>
</div>
<div>I got an error message about this: </div>
<div>ERROR: Temporary directory set to an NFS location.</div>
<div>TMP=/home/lin11/tmp</div>
<div>The temporary directory in MAKER is specifically for</div>
<div>operations that are not NFS-safe. You must set TMP</div>
<div>to a locally mounted directory such as /tmp or add</div>
<div>--ignore_nfs_tmp to the maker command line to</div>
<div>override this error message.</div>
<div><br>
</div>
<div>Does the MAKER need a big temporary file? Because our system temporary directory may not have that much space. If it does not need that big tmp file, I can set it back to default. Or I just ignore the error message? </div>
<div><br>
</div>
<div>Thank you.</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Yunxi Lin <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
<div dir="ltr">Thank you.</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Anything from maker under the ~/perl5/ should be deleted. MAKER should be self contained in its own directory. Do 'rm ~/perl5/bin/*maker*'. If you see anything else that is maker related there delete it as well.</div>
<div><br>
</div>
<div>Example:</div>
<div>.../maker/bin/</div>
<div>.../maker/lib/</div>
<div>.../maker/exe/</div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
</div>
<div><br>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 1:40 PM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div><br>
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<div dir="ltr">Hi Carson
<div><br>
</div>
<div>I installed the new version of MAKER. But right now have a problem of running it. Because I was missing perl dependencies, I installed the perl local library. And then I tried to run maker, it will automatically go to the one in local library called ~/perl5/bin/maker.
Do you know how to get rid of this path? I found this path in .bashrc : export PATH="/home/lin11/perl5/bin:$PATH". If that ok to delete it?</div>
<div><br>
</div>
<div>Thank you.</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>It's been stable enough that I could remove the beta tag (no major updates in 2 months). In fact I'll go ahead and do that.</div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
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<span>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 12:21 PM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div><br>
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<div dir="ltr">Hi Carson
<div><br>
</div>
<div>Is that the 2.28 only have the beta version?</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Yunxi Lin <span dir="ltr"><<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thank you Carson. I'll try then let you know.</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>You could just install it in a new directory (I.e. maker_2.28 rather than maker). The 2.1 version more than 2 years old (lots of changes and improvements since then).</div>
<div><br>
</div>
<div>--Carson</div>
<div><br>
</div>
<div><br>
</div>
<span>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 12:11 PM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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</div>
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<div><br>
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<div dir="ltr">Hi Carson
<div>I think I may need to update MAKER too. My version is 2.1. Is the new version of MAKER changed a lot? Because someone running MAKER on the server now, can I just update it instead of delete the old one then reinstall the new version? </div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>If you are using MAKER 2.28, and let it do the install for you it will install mpich2 from this location --> <a href="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz" target="_blank">http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz</a></div>
<div><br>
</div>
<div>The installation will be in the .../maker/exe/mpich2 directory.</div>
<div><br>
</div>
<div>Alternatively, if you do the installation yourself, all you have to do set a few flags during install configuration.</div>
<div>--> ./configure --prefix=$path --enable-shared</div>
<div>Set $path to the location where you want MPICH2 to be installed.</div>
<div>Then run 'make install'</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
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<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 11:59 AM
<div>
<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div><br>
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<div dir="ltr">Hi Carson
<div><br>
</div>
<div>I think it installed the 1.3.1 version. Can I update it?</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/7/2 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>It should be installed under .../maker/exe/mpich2. Having it under ~/perl5/exe/mpich2 is odd as maker should do that.</div>
<div><br>
</div>
<div>Type 'which mpiexec' to see if there is another mpiexec installed somewhere. Also run 'mpiexec --version'. What does it give? I ask because the error message you got before is the same as a bug in an old version of MPICH2 (version 1.3). MAKER will
install version 1.5.</div>
<div><br>
</div>
<div>Also run 'mpiexec -n 16 hostname'</div>
<div>What happens?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
</div>
<div><br>
</div>
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<span style="font-weight:bold">From: </span>csusm <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, July 2, 2013 11:17 AM
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<div><br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div>Hi Carson</div>
<div><br>
</div>
<div>How's the trip?</div>
<div><br>
</div>
<div>I did it followed your instruction. I ran ./build mpich2 first</div>
<div>It installed it into ~/perl5/exe/mpich2 directory. </div>
<div>And then i go back to maker/src ran perl <a href="http://build.pl" target="_blank">
build.pl</a> and type Y to accept the MPI. </div>
<div>Then I ran ./build install</div>
<div>After that, I went to ~/.bash_profile to add the ~/perl5/exe/mpich2/bin into the PATH. </div>
<div>I used mpiexec -n 16 maker as the command. </div>
<div>Do I need to set some special variable in that three control file first? </div>
<div><br>
</div>
<div>Thank you. </div>
<div><br>
Yunxi Lin</div>
<div><br>
On Jul 2, 2013, at 7:44 AM, Carson Holt <<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>> wrote:<br>
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<blockquote type="cite">
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<div>Sorry for not responding sooner (it was a long holiday weekend in Canada). Did you have maker install MPICH2 or did you install it yourself? Also what is the exact command line you used to launch?</div>
<div><br>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, June 30, 2013 2:09 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
<div><br>
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<div>I got the errors like:</div>
<div>
<div>[mpiexec@bioinfo1] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file hydra_pmi_proxy (No such file or directory)</div>
<div>[mpiexec@bioinfo1] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:315): assert (!closed) failed</div>
<div>[mpiexec@bioinfo1] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status</div>
<div>[mpiexec@bioinfo1] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event</div>
<div>[mpiexec@bioinfo1] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion</div>
<div><br>
</div>
<div>Is that means our server only has one cpu so I cannot use mpi? </div>
<div><br>
</div>
<div>Thank you.</div>
</div>
<div><br>
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<div class="gmail_extra"><br>
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<div class="gmail_quote">2013/6/25 Carson Holt <span dir="ltr"><<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
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<div>
<div>You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.</div>
<div><br>
</div>
<div>When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only). It will be in …/maker/exe/mpich2. This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having
to get upgraded privileges. So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.</div>
<div><br>
</div>
<div>--Carson</div>
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<span style="font-weight:bold">From: </span>csusm <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 25 June, 2013 11:40 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>>
<div>
<div><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div>Hi Carson</div>
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<div>Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu? Because my school own the server, I only have the limit authorization. <br>
<br>
Yunxi Lin</div>
<div><br>
On Jun 24, 2013, at 5:39 PM, Carson Holt <<a href="mailto:Carson.Holt@oicr.on.ca" target="_blank">Carson.Holt@oicr.on.ca</a>> wrote:<br>
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<div>
<div>You are most likely only getting 1 cpu of performance.</div>
<div><br>
</div>
<div>You should just install MPICH2. It's easy just to let MAKER do it for you:</div>
<div><span style="white-space:pre-wrap"></span>Go to the …/maker/src/ directory</div>
<div><span style="white-space:pre-wrap"></span>Run './Build mpich2'</div>
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<div>
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<div>Once it finishes installing, it will be in the …/maker/exe/mpich2/bin/ directory.</div>
<div><br>
</div>
<div>Setup MAKER again to use MPICH2:</div>
<div><span style="white-space:pre-wrap"></span>Go to the …/maker/src/ directory</div>
<div><span style="white-space:pre-wrap"></span>Run 'perl Build.PL'</div>
<div><span style="white-space:pre-wrap"></span>Say yes to the "use MPI": question</div>
<div><span style="white-space:pre-wrap"></span>Run './Build install'</div>
<div><br>
</div>
<div>Now run MAKER via 'mpiexec'.</div>
<div><span style="white-space:pre-wrap"></span>Example --> …/maker/exe/mpich2/bin/mpiexec -n 16 maker</div>
<div><br>
</div>
<div>The –n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines. You will get much better performance.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Carson</div>
<div><br>
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<div><br>
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<span style="font-weight:bold">From: </span>Yunxi Lin <<a href="mailto:lin11@cougars.csusm.edu" target="_blank">lin11@cougars.csusm.edu</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 24 June, 2013 7:11 PM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span>Amelia Ireland <<a href="mailto:amelia.ireland@gmod.org" target="_blank">amelia.ireland@gmod.org</a>>, <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] Fwd: about running MAKER<br>
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<div dir="ltr">Hi Carson
<div><br>
</div>
<div>Thank your for your help. </div>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>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>
<div><br>
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<div>Sincerely,</div>
<div>Yunxi</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<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>
<div><br>
</div>
<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>
<div><br>
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<div>--Carson</div>
<div><br>
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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>
</div>
<div>
<div>
<div><br>
</div>
<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>
<br>
<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>
<br>
<br>
<div dir="ltr"><span style="font-size: 14px; font-family: arial, sans-serif; ">Hi </span>
<div style="font-family:arial,sans-serif;font-size:14px"><br>
</div>
<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>
<div style="font-family:arial,sans-serif;font-size:14px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:14px">Thank you. </div>
<div style="font-family:arial,sans-serif;font-size:14px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:14px">Sincerely,</div>
<div style="font-family:arial,sans-serif;font-size:14px">Lin</div>
</div>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <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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