<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>That is one I haven't seen before (including on large multi-megabase contigs ).</div><div><br></div><div>Right before the error, it will say the location of the file that is being read. It will terminate in ".augustus". Could you send that file to me? Augustus seems to be producing something weird in it's output.</div><div><br></div><div>Thanks,</div><div>Carson</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> Friday, 8 June, 2012 12:15 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<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] cluster error running maker<br></div><div><br></div>Hi Carson,<div><br></div><div>I will try this as well to get my 2.25 version of maker running.</div><div><br></div><div>I have hit another error on my local machine. This only seems to come up with scaffolds > 5Mbp. And am hitting this same error with version 2.10 and 2.25.</div><div><br></div><div><div> [0] = Make</div><div> [1] = 0</div><div> [2] = additional</div><div> [3] = prediction</div><div> [4] = runs.</div><div>dead in Widget::augustus::parse_gene unknown feature type:additional</div><div>ERROR: Failed while preparing ab-inits</div><div>ERROR: Chunk failed at level:4, tier_type:0</div><div>FAILED CONTIG:GL343198.1</div><div><br></div><div>Do you have a suggestion for this one?</div><div><br></div><div>
Thanks for all your help,</div><div><br></div><div>Walter</div><div><br></div><br><div class="gmail_quote">On 8 June 2012 05:45, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><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 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><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Walter Eckalbar <<a href="mailto:weckalba@asu.edu" target="_blank">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" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] cluster error running maker<br></div><div><div class="h5"><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></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span></div></blockquote></div><br></div></span></body></html>