<div dir="ltr"><div>Thanks for the help guys. All really helpful!</div><div><br></div>Unfortunately, full Perl reinstall is not an option at this moment on this machine, since it's used by others in our group and they need it running... I'll try to find another solution with our admin.</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jul 15, 2014 at 4:10 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>If you don't have MPI support, it's not an issue, and your Seg fault is likely something else. Your reference to perl 5.18 and <a href="http://forks.pm" target="_blank">forks.pm</a> should not be a segfault error either, and would not represent your error. The Perl 5.18/<a href="http://forks.pm" target="_blank">forks.pm</a> is a different issue where perl actually tells itself to die because hash reshuffling isn't safe whereas segfaults are causes by binary corruption or incorrect memory access issues (very different issues). I'd actually recommend a full perl reinstall if you are getting segfaults, because it suggests a deeper issue.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, July 15, 2014 at 8:03 AM<div>
<div class="h5"><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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>>, maker-devel <<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] (no subject)<br></div></div></div><div><div class="h5"><div><br></div><div dir="ltr">Carson, many thanks for the info!<div><br></div><div>I haven't installed Maker with MPI support. Is this segfault only occurring when you install it with MPI support?</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jul 15, 2014 at 3:58 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px"><div style="font-family:Calibri,sans-serif">If you are getting a segfault. It is more likely an MPI error especially if you are using OpenMPI or MVAPICH2. They both use OpenFabrics libraries that have bugs on forks and system calls.</div>
<div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif">If it is OpenMPI, run the following command before launching MAKER --></div><div><span style="font-size:medium"><font face="Courier"><span style="white-space:pre-wrap"> </span>export LD_PRELOAD=Š/openmpi_location/lib/libmpi.so</font></span></div>
<div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif">Make sure to set replace openmpi_location with the location of your OpenMPI.</div><div style="font-family:Calibri,sans-serif">
<br></div><div style="font-family:Calibri,sans-serif">Also add the following to your MPI command before running MAKER.</div><div><div><font face="Calibri,sans-serif">--> </font><font face="Courier">-mca btl ^openib</font></div>
<div><span style="font-family:Calibri,sans-serif">Example --> </span><font face="Courier">mpiexec -mca btl ^openib -n 40 maker</font></div></div><div><br></div><div><br></div><div>If you are using MVAPICH2, then you need to switch to OpenMPI.</div>
<div><br></div><div>--Carson</div><div> </div><div><br></div><div><br></div><div><br></div><span style="font-family:Calibri,sans-serif"><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, July 15, 2014 at 12:59 AM<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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>>, maker-devel <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><div>
<div><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] (no subject)<br></div></div></div><div><div><div><br></div><div dir="ltr">I didn't know there are more than one <a href="http://forks.pm" target="_blank">forks.pm</a> files! We'll give it another try later today.<div>
<br></div><div>As for the error, it's just "Segmentation fault"! And we know this segfault is because of <a href="http://forks.pm" target="_blank">forks.pm</a>, because if you remove the "use forks;" line script execution continues without segfault (till it crashes later for another reason, of course). In fact, even if you create a script with just the line "use forks;" and try to run it, you'll get a segfault. So it looks like it's something pretty general and serious, and I'm really surprised I can't find anything by googling (except your fix!)...</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 14, 2014 at 4:49 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Also one more question. What is the exact error text you get for the forks error? Is it a <a href="http://forks.pm" target="_blank">forks.pm</a> error or is it an MPI warn on fork error (which are actually very different).</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, July 14, 2014 at 8:46 AM<br>
<span style="font-weight:bold">To: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>>, Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><div>
<div><br><span style="font-weight:bold">Cc: </span> maker-devel <<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] (no subject)<br>
</div></div></div><div><div><div><br></div><div><div style="word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">If you do the BLAST's yourself the results could be dramatically worse. The filtering and polishing done by MAKER is rather significant (direct BLAST is actually worse with homology searches than many people realize).</div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">With respect to <a href="http://forks.pm" target="_blank">forks.pm</a>, your admin most likely edited the wrong <a href="http://forks.pm" target="_blank">forks.pm</a>. There may be more than one on your system. If you let maker install some prerequisites for you (because it requires a specific version of <a href="http://forks.pm" target="_blank">forks.pm</a>), it may be in .../maker/perl/lib/<a href="http://forks.pm" target="_blank">forks.pm</a>. Otherwise you have to identify the exact location of the <a href="http://forks.pm" target="_blank">forks.pm</a> being used. Or if he is editing it as part of the install tarball, his edits may actually be undone during the installation procedure.</div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">Use this command line to identify the location of the <a href="http://forks.pm" target="_blank">forks.pm</a> module that would have to be edited --></div>
<div style="color:rgb(0,0,0);font-size:14px"><font face="Courier">maker --debug 2>&1 | grep "<a href="http://forks.pm" target="_blank">forks.pm</a>"</font></div><div><font face="Calibri,sans-serif"><br></font></div>
<div><font face="Calibri,sans-serif">You can even send me a copy of the file once it has been edited, and I can tell you if it was done correctly.</font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">--Carson</font></div>
<div><font face="Calibri,sans-serif"><br></font></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br>
</div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><br></div><span style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span> Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, July 14, 2014 at 1:20 AM<br>
<span style="font-weight:bold">To: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Cc: </span> maker-devel <<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] (no subject)<br></div><div><br></div><div dir="ltr">Daniel, thanks for the info.<div><br></div><div>Regarding (3), the only reason I think of running BLASTs separately is because I'm currently not able to run Maker on our cluster due to a problem in the Perl "forks" library. And it looks like there isn't much I can do about it; I tried Perlbrew but it doesn't work when I try to install versions <5.18 (the problem in forks occurs on 5.18 and later versions). Our admin also tried to change the code in the <a href="http://forks.pm" target="_blank">forks.pm</a> file as per Carson's suggestion in another thread, but that didn't work either... As a result I'm running Maker on my workstation (really slooow) till a solution is found and since BLAST is a time-consuming step I was thinking of running it separately.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jul 11, 2014 at 4:08 PM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi Panos,
<div><br></div><div>1) You'll only use est2genome and protein2genome for creating models that will be used for training the ab-initio predictors (like SNAP). Sometimes that means one run of MAKER for training; sometimes that means two runs of MAKER. You usually don't gain
any accuracy after the second round of training. It's ok to use both EST and protein data for this training step. </div><div><br></div><div>2) If you're using both ESTs and protein sequence to train your ab-initio predictors, then both est2genome and protein2genome should be set to 1. </div>
<div><br></div><div>3) If you want to pass Blast results to MAKER, you'll need to pass those results as GFF3, but MAKER will install and run blast for you, and does a good job of keeping track of all those results and making them accessible to you in the end, so it's going
to be a lot of work to do those blasts on your own outside of MAKER. I seriously suggest that you use blast internal to maker. <br><div><br><div><font><div>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></font></div></div><div style="font-family:Times New Roman;color:#000000;font-size:16px"><hr><div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of Panos Ioannidis [<a href="mailto:panos.ioannidis@gmail.com" target="_blank">panos.ioannidis@gmail.com</a>]<br>
<b>Sent:</b> Friday, July 11, 2014 5:56 AM<br><b>To:</b> maker-devel<br><b>Subject:</b> [maker-devel] (no subject)<br></font><br></div><div><div><div></div><div><div dir="ltr">I got back to my annotations this past week and have a couple of questions!
<div><br></div><div>1) Since my organism isn't closely related with any other that's already sequenced, I will have to run maker twice (according to the tutorial). So for the first run I see that some people use only the ESTs and some others use ESTs and a protein database
(CEGMA, Uniref50, Swiss-Prot, etc). I guess that the ESTs will give better models, but for the cases where genes aren't covered by an EST, it's okay to have a protein database to detect them as well. Am I right? What do you think?</div>
<div><br></div><div>2) In case I use both ESTs and a protein database how should I set the <font face="courier new,monospace">
est2genome</font> and <font face="courier new,monospace">protein2genome</font> parameters in the
<font face="courier new,monospace">maker_opts.ctl</font> file? Should they both equal to "1"?</div><div><br></div><div>3) I've been thinking of running the BLAST searches separately and giving Maker directly the results. I guess that in this case, I'll have to first convert the BLAST output to a gff3 file and give it to the
<font face="courier new,monospace">protein_gff</font> parameter, right?</div><div><br></div><div>Thanks,</div><div>Panos</div></div></div></div></div></div></div></div></div></blockquote></div><br></div>
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