<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>I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --></div><div>WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC</div><div><br></div><div>Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well.</div><div>That is why you get --></div><div><div><div><font face="courier new,monospace">------------- EXCEPTION: Bio::Root::Exception -------------</font></div></div><div><div><font face="courier new,monospace">MSG: Sequence is a protein. Cannot revcom</font></div></div></div><div><br></div><div>You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file.</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 23 November, 2012 3:06 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> 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>Thanks for your reply, and sorry for my delayed response.<div><br></div><div>I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else.</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 Mon, Nov 12, 2012 at 10:02 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;word-wrap:break-word"><div style="font-family:Calibri,sans-serif">The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file <span style="font-family:Calibri">--> <span style="font-family: 'courier new', monospace; ">/N/dc/scratch/dstandag/PdomGenomic/Annotation/</span><span style="font-family: 'courier new', monospace; ">output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se</span><span style="font-family: 'courier new', monospace; ">q93.est_exonerate.0</span></span></div><div><span style="font-family: 'courier new', monospace; "><br></span></div><div>This one --><span style="font-family: 'courier new', monospace; "> </span><span style="font-family: 'courier new', monospace; ">/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta</span></div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif">And this one --> <span style="font-family: 'courier new', monospace; ">/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta</span></div><div style="font-family:Calibri,sans-serif"><span style="font-family: 'courier new', monospace; "><br></span></div><div>thanks,</div><div>Carson</div><div style="font-family:Calibri,sans-serif"><span style="font-family: 'courier new', monospace; "><br></span></div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif"><br></div><span style="font-family: Calibri, sans-serif; "><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> Thursday, 8 November, 2012 9:32 AM<div><div class="h5"><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><div class="h5"><div><br></div>Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error...<div><br></div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div><div><font face="courier new,monospace">#-------------------------------#</font></div></div><div><div><font face="courier new,monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div></div><div><div><font face="courier new,monospace">running est2genome search.</font></div></div><div><div><font face="courier new,monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new,monospace">Widget::exonerate::est2genome:</font></div></div><div><div><font face="courier new,monospace">/N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0</font></div></div><div><div><font face="courier new,monospace">#-------------------------------#</font></div></div><div><div><font face="courier new,monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div></div><div><div><font face="courier new,monospace">couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60.</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 polishig ESTs</font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:2, tier_type:2</font></div></div><div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_23</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_23</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></blockquote><div><br></div><div><br></div><div>...as well as one occurrence of this error.</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><font face="courier new,monospace">#-------------------------------#</font></div></div><div><div><font face="courier new,monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div></div><div><div><font face="courier new,monospace">running est2genome search.</font></div></div><div><div><font face="courier new,monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new,monospace">Widget::exonerate::est2genome:</font></div></div><div><div><font face="courier new,monospace">/N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd</font></div></div><div><div><font face="courier new,monospace">om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno</font></div></div><div><div><font face="courier new,monospace">tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta </font></div></div><div><div><font face="courier new,monospace">-Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/</font></div></div><div><div><font face="courier new,monospace">output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se</font></div></div><div><div><font face="courier new,monospace">q93.est_exonerate.0</font></div></div><div><div><font face="courier new,monospace">#-------------------------------#</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">------------- EXCEPTION: Bio::Root::Exception -------------</font></div></div><div><div><font face="courier new,monospace">MSG: Sequence is a protein. Cannot revcom</font></div></div><div><div><font face="courier new,monospace">STACK: Error::throw</font></div></div><div><div><font face="courier new,monospace">STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368</font></div></div><div><div><font face="courier new,monospace">STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381</font></div></div><div><div><font face="courier new,monospace">STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577</font></div></div><div><div><font face="courier new,monospace">STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/<a href="http://splice_info.pm:86" target="_blank">splice_info.pm:86</a></font></div></div><div><div><font face="courier new,monospace">STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/<a href="http://est2genome.pm:686" target="_blank">est2genome.pm:686</a></font></div></div><div><div><font face="courier new,monospace">STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/<a href="http://est2genome.pm:961" target="_blank">est2genome.pm:961</a></font></div></div><div><div><font face="courier new,monospace">STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/<a href="http://est.pm:82" target="_blank">est.pm:82</a></font></div></div><div><div><font face="courier new,monospace">STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/<a href="http://est.pm:44" target="_blank">est.pm:44</a></font></div></div><div><div><font face="courier new,monospace">STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670</font></div></div><div><div><font face="courier new,monospace">STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517</font></div></div><div><div><font face="courier new,monospace">STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663</font></div></div><div><div><font face="courier new,monospace">STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335</font></div></div><div><div><font face="courier new,monospace">STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351</font></div></div><div><div><font face="courier new,monospace">STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286</font></div></div><div><div><font face="courier new,monospace">STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286</font></div></div><div><div><font face="courier new,monospace">STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644</font></div></div><div><div><font face="courier new,monospace">-----------------------------------------------------------</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 polishig ESTs</font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:2, tier_type:2</font></div></div><div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_7</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_7</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></blockquote><div><br></div><div>I'll let you know if I see anything else.</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 11:46 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. Typo now fixed on my end too ;-)</div><div><br></div><div>Thanks,</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> Wednesday, 7 November, 2012 11:43 AM<div><div><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><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><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><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></div></div></span></div></blockquote></div><br></div></div></div></span></div></blockquote></div><br></div></span></body></html>