<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>Thanks. Typo now fixed on my end too ;-)</div><div><br></div><div>Thanks,</div><div>Carson</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 7 November, 2012 11:43 AM<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> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: Maker issues<br></div><div><br></div>Looked good for a while, but came across this error.<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><font face="courier new,monospace">total clusters:20 now processing 0</font></div></div><div><div><font face="courier new,monospace">flattening EST clusters</font></div></div><div><div><font face="courier new,monospace">doing tblastx of alt-ESTs</font></div></div><div><div><font face="courier new,monospace">Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648.</font></div></div><div><div><font face="courier new,monospace">--> rank=NA, hostname=c4</font></div></div><div><div><font face="courier new,monospace">ERROR: Failed while doing tblastx of alt-ESTs</font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:4, tier_type:2</font></div></div><div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_58</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:5, tier_type:0</font></div></div><div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_58</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">examining contents of the fasta file and run log</font></div></div><div><div><font face="courier new,monospace">Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new,monospace">Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new,monospace">Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">--Next Contig--</font></div></div></blockquote><div><br></div><div>It seems pretty clear that there is a typo in GI.pm. I changed <b>loalize</b> to <b>localize</b> and relaunched.</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 9:30 AM, Daniel Standage <span dir="ltr"><<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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"><div class="im"><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><div><div class="h5"><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><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></blockquote></div><br></div></div></div></span></div></blockquote></div><br></div></div></div></blockquote></div><br></div></span></body></html>