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>
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