<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).<div><br></div><div>Something like this should work to force indexing:</div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_keyword"><br></span></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_keyword">use</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> Bio</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">::</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">DB</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">::</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; ">Fasta</span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">;</span></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_keyword">my</span> <span class="sh_variable">$db</span> <span class="sh_symbol">=</span> Bio<span class="sh_symbol">::</span>DB<span class="sh_symbol">::</span>Fasta<span class="sh_symbol">-></span><span class="sh_function">new</span><span class="sh_symbol">(</span><span class="sh_string">'/path/to/fasta/files'</span><span class="sh_symbol">);</span></span></div><div><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_keyword">my</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> </span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_variable">$seq</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> </span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">=</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "> </span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_variable">$db</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">-></span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_function">seq</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">($</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_string">seqid</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">, $start, $end</span></span><span class="Apple-style-span" style="font-family: monospace; white-space: pre; "><span class="sh_symbol">);</span></span></div><div><div><br></div></div><div>Point it at your fasta directory or file.</div><div><br></div><div>B</div><div><br><div><div>On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>We reinstalled the packages you suggested<br><br>forks is up to date (0.34).<br>forks::shared is up to date (0.34).<br>Inline::C is up to date (0.50).<br>Storable is up to date (2.30).<br><br>as well as BioPerl.<br><br>The problem is still the same.<br><br>With MPI it terminates with this message:<br><br>STATUS: Parsing control files...<br>STATUS: Processing and indexing input FASTA files...<br>===================================================================================== <br><br>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>= EXIT CODE: 11<br>= CLEANING UP REMAINING PROCESSES<br>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>===================================================================================== <br>APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)<br><br>which I presume is also the same problem.<br><br>I am with you that the error is caused somewhere on the C level. If the indexing step<br>is handled by non-maker modules exclusively, than the fact that the 2.15 version works,<br>suggests that you are using different modules/methods in the current releases?<br><br>In any case, I think a version with verbose status messages might help to localize the<br>source of the problem.<br><br>Regards<br>Thomas<br><br>Am 07.03.2012 23:45, schrieb Carson Holt:<br><blockquote type="cite">There should be no new hardware requirement. But there is always a chance<br></blockquote><blockquote type="cite">that there is an issue with one of the perl modules being used. I assume<br></blockquote><blockquote type="cite">the failure is happening when using maker serially and you are not using<br></blockquote><blockquote type="cite">MPI.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Could you reinstall the following perl modules, and try again. If you are<br></blockquote><blockquote type="cite">using CPAN, do a 'force install' to force it to reinstall.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Modules:<br></blockquote><blockquote type="cite">*Storable<br></blockquote><blockquote type="cite">*Inline::C<br></blockquote><blockquote type="cite">*forks<br></blockquote><blockquote type="cite">*forks::shared<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Also try reinstalling the latest version of BioPerl.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The fact that this is a seg fault suggests that something is happemning at<br></blockquote><blockquote type="cite">the C level (just outside of Perl). Those area all the modules MAKER uses<br></blockquote><blockquote type="cite">that will call back to the C level. BioPerl has a fasta indexing module<br></blockquote><blockquote type="cite">that is also making calls outside of Perl, and the fact it fails at that<br></blockquote><blockquote type="cite">point makes it a suspect.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Let me know what happens. I can always generate an alternate MAKER<br></blockquote><blockquote type="cite">executable for you to run with additional status messages that may help<br></blockquote><blockquote type="cite">identify exactly which module is being called right before the failure.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Carson<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 12-03-07 3:31 AM, "Thomas Hackl"<<a href="mailto:thomas.hackl@uni-wuerzburg.de">thomas.hackl@uni-wuerzburg.de</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hello,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">we want to use a current release of maker (2.22, 2.23) but the program<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">terminates with a seg fault while processing the input FASTA files.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">maker 2.15 , which we have been using for quite some time, runs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">perfectly with identical data and setup.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Please contact me if you need specifics on hardware, OS or anything else.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Best regards<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thomas<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-- <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thomas Hackl<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Julius-Maximilians-Universität<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Department of Bioinformatics<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">97074 Würzburg, Germany<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Fon: +49 931 - 31 86883<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Mail: <a href="mailto:thomas.hackl@uni-wuerzburg.de">thomas.hackl@uni-wuerzburg.de</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">maker-devel mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><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><br></blockquote></blockquote><br><br>-- <br>Thomas Hackl<br>Julius-Maximilians-Universität<br>Department of Bioinformatics<br>97074 Würzburg, Germany<br>Fon: +49 931 - 31 86883<br>Mail: <a href="mailto:thomas.hackl@uni-wuerzburg.de">thomas.hackl@uni-wuerzburg.de</a><br><br><br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div apple-content-edited="true">
<div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div><br class="Apple-interchange-newline">
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