<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>Here is a patch for the Proc::ProcessTable module in Perl. Thanks to Volker Brendel at Iowa State for this one.</div><div><br></div><div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div style="font-family: Consolas; font-size: medium; ">Apply in Proc-ProcessTable-0.45 directory with --> patch -np1 < 646785-and-handle-Hex29.patch</div><div style="font-family: Consolas; font-size: medium; "><br></div><div style="font-family: Consolas; font-size: medium; ">This adds to previously posted 646785 patch. At least on some systems, commands can contain "(" and ")". See comments in the code.</div><div style="font-family: Consolas; font-size: medium; "><br></div></blockquote></div><div><br></div><div>Download <span class="Apple-style-span" style="font-family: Consolas; font-size: medium; ">Proc-ProcessTable-0.45 to reinstall before applying the patch.</span></div><div><br></div><div><br></div><div>I'll also send you a link in a separate e-mail to download a maker 2.26 test version where I've replaced Proc::ProcessTable with a different module because of the failure on some systems.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></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> Walter Eckalbar <<a href="mailto:weckalba@asu.edu">weckalba@asu.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 7 June, 2012 4:40 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] cluster error running maker<br></div><div><br></div>Hi everyone,<div><br></div><div>I have been retrying installing maker on our university cluster, everything seems to install correctly, but when I run maker I find the following error message:</div><div><br></div><div><div>
Ran into unknown state (hex char: 29) at /home/weckalba/RNAseq/maker/lib/File/..//Proc/Signal.pm line 94.</div><div>A data structure will be created for you at:</div><div>/scratch/weckalba/Maker/genome.maker.output/genome_datastore</div><div><br></div><div>To access files for individual sequences use the datastore index:</div><div>/scratch/weckalba/Maker/genome.maker.output/genome_master_datastore_index.log</div><div><br></div><div>DBD::SQLite::db do failed: disk I/O error at /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 88.</div><div>DBD::SQLite::db selectcol_arrayref failed: disk I/O error at /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 90.</div><div>DBD::SQLite::db do failed: disk I/O error at /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 92.</div><div>DBD::SQLite::db do failed: disk I/O error at /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 161.</div></div><div><br></div><div><br></div><div>Seems to have something to do with permissions and DBD::SQLite. I installed DBD::SQLite on my own home directories and routed the perl path to it (and other CPAN installs in the same directories).</div><div><br></div><div>I was wondering if anyone ever encountered this before and knew a work around. The admins for our cluster are unfortunately very slow to respond.</div><div><br></div><div>Thanks</div><div><br></div><div>
Walter</div>
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