<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; 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 forks.pm 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 id="OLK_SRC_BODY_SECTION"><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">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">panos.ioannidis@gmail.com</a>>, Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Cc: </span> maker-devel <<a href="mailto:maker-devel@yandell-lab.org">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><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><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 forks.pm, your admin most likely edited the wrong forks.pm. 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 forks.pm), it may be in .../maker/perl/lib/forks.pm. Otherwise you have to identify the exact location of the forks.pm 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 forks.pm 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 "forks.pm"</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 id="OLK_SRC_BODY_SECTION" 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">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">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Cc: </span> maker-devel <<a href="mailto:maker-devel@yandell-lab.org">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">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 class="h5"><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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