<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); "><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Segmentation fault means there was a failure with C code. It was likely in one of the modules being used.</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">These are all potential culprits</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Inline::C</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Proc::ProcessTable</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">DB_file</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">forks</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Based on when the error occurred. I would lean more toward DB_File. Is it possible that BerkleyDB has been updated on your system, perhaps as part of another installation or a system update? That sometimes breaks this module (which is part of the perl core).</span></div><div><font class="Apple-style-span" face="Tahoma"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">You can try reinstalling that module from CPAN. Also if you run MAKER version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug') to get more information just before the error occurs. You can then capture the error log send that to me.</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Thanks,</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Carson</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; 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> Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span> Tue, 17 Apr 2012 16:46:40 +0000<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] MAKER2.23 output<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style type="text/css" id="owaParaStyle"></style><div fpstyle="1" ocsi="0"><div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,
<div><br></div><div>I tried running the latest version of Maker 2.23 with my dataset but with out much success.</div><div><br></div><div>When I run it without the mpi option I exits with a segmentation fault</div><div><br></div><div><div>STATUS: Processing and indexing input FASTA files...</div><div>Segmentation fault</div></div><div><br></div><div>So, I tried it with mpi, the run does start but I don't see any output files. I ran it with 20 cpus for close to 10 hrs </div><div><br></div><div>I tested this with the sample data in maker's data folder. </div><div><br></div><div>Input in maker_opts.ctl file</div><div><br></div><div>genome=/usr/local/maker/2.23/data/dpp_contig.fasta</div><div>est= /usr/local/maker/2.23/data/dpp_est.fasta</div><div>protein= /usr/local/maker/2.23/data/dpp_protein.fasta</div><div>est2genome=1</div><div><br></div><div>This was the command I executed</div><div><br></div><div>usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2 /usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl</div><div><br></div><div>The following folder with the protein sequence file gets created</div><div><br></div><div>dpp_contig.maker.output</div><div><br></div><div>But I can't see any progress after that.</div><div><br></div><div>Can you please tell me if I might be doing something wrong or need further details</div><div><br></div><div>I was able run the previous version of Maker 2.10 successfully with my dataset.</div><div><br></div><div>Thanks,</div><div>Ranjani</div><div><br></div><div><br></div></div></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>