<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Great to know it’s working for you now.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 24, 2016, at 11:11 AM, Seth Munholland <<a href="mailto:munholl@uwindsor.ca" class="">munholl@uwindsor.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Carson,<br class=""><br class=""></div>Just an update, that was indeed my issue. Thanks for your help!<br class=""></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature"><div dir="ltr" class=""><div class="">Seth Munholland, B.Sc.<br class=""></div><div class="">Department of Biological Sciences<br class="">
Rm. 304 Biology Building<br class="">
University of Windsor<br class="">
401 Sunset Ave. N9B 3P4<br class="">
T: <a value="+15192533000" class="">(519) 253-3000 Ext: 4755</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Wed, May 11, 2016 at 11:35 AM, Seth Munholland <span dir="ltr" class=""><<a href="mailto:munholl@uwindsor.ca" target="_blank" class="">munholl@uwindsor.ca</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="">Hi Carson,<br class=""><br class=""></div>I am not using an MPI. Given the association to tblastx I suspect my c++ install of BLAST is what's seg faulting. Thanks!<br class=""></div><div class="gmail_extra"><span class=""><br clear="all" class=""><div class=""><div class=""><div dir="ltr" class=""><div class="">Seth Munholland, B.Sc.<br class=""></div><div class="">Department of Biological Sciences<br class="">
Rm. 304 Biology Building<br class="">
University of Windsor<br class="">
401 Sunset Ave. N9B 3P4<br class="">
T: <a value="+15192533000" class="">(519) 253-3000 Ext: 4755</a></div></div></div></div>
<br class=""></span><div class=""><div class="h5"><div class="gmail_quote">On Tue, May 10, 2016 at 7:02 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">So MAKER is written in Perl, and Perl can’t really seg fault (it doesn’t give developers that kind of low level access to memory). However if you are using MPI, then it could be causing a seg fault, or one of the programs MAKER is calling could be seg faulting (like BLAST).<div class=""><br class=""></div><div class="">So if you are using MPI, let me know which flavor and I can make suggestions (for example MVAPICH2 is incompatible with programs that do system calls, and OpenMPI may require special setting for LD_PRELOAD to work properly with shared libraries). If your not using MPI, then you will need to look at the installed programs MAKER is calling and reinstall them, update them, or roll back a version (i.e. BLAST, Exonerate, etc.)</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class=""><div class="">On May 10, 2016, at 12:18 PM, Seth Munholland <<a href="mailto:munholl@uwindsor.ca" target="_blank" class="">munholl@uwindsor.ca</a>> wrote:</div><br class=""></div></div><div class=""><div class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">Hello Everyone,<br class=""><br class=""></div>For reasons unknown my MAKER (2.31.8 on Ubuntu 14.04) runs keep seg faulting. I've changed the the dataset I'm running MAKER on, by parsing out smaller sections of the larger assembly, and I still seg fault on sections that the larger assembly moved past without issue.<br class=""><br class=""></div>The only commonality I see is every tme it seg faults it appears to have jsut finished a tblastx. Any suggestions for how I can debug and correct this issue?<br class=""><div class=""><div class=""><br clear="all" class=""><div class=""><div class=""><div class=""><div dir="ltr" class=""><div class="">Seth Munholland, B.Sc.<br class=""></div><div class="">Department of Biological Sciences<br class="">
Rm. 304 Biology Building<br class="">
University of Windsor<br class="">
401 Sunset Ave. N9B 3P4<br class="">
T: <a value="+15192533000" class="">(519) 253-3000 Ext: 4755</a></div></div></div></div>
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