Done.<div><br></div><div>Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks!</div><div class="gmail_extra"><br clear="all">
<br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br>
<br><br><div class="gmail_quote">On Wed, Nov 7, 2012 at 9:00 AM, 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>1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm</div><div><br></div><div>
One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl.</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 5 November, 2012 10:14 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: Maker issues<br></div><div><div class="h5"><div><br></div>Debug output attached (bzip2 compressed).<div class="gmail_extra"><br clear="all"><br>--<br>Daniel S. Standage<br>
Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br><br><br><br><div class="gmail_quote">On Mon, Nov 5, 2012 at 10:08 AM, 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>Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that.</div>
<div><br></div><div>--Carson</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 5 November, 2012 10:05 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>, Maker Mailing List <<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 issues<br></div><div><div><div><br></div>Carson,<div><br></div><div>I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version.<br clear="all">
<br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br></div></div></div></span></div>
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