<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Make sure you installed the CPAN version of BioPerl and not BioPerl live (Current version is 1.6.924). Also there are a couple of BLAST+ versions that have bugs. Use version BLAST+ version 2.2.28. What version of MAKER are you using? Should be 2.31.8. Also check that your /tmp directory is not full (will result in truncated output files).<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 9:56 PM, Sok Lim Chew <<a href="mailto:14.chewsoklim@gmail.com" class="">14.chewsoklim@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8px" class="">Hi all,</span><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">The following errors occurred while I was using MAKER for annotation. I have searched around this forum but seems like the solutions provided do not works for me.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">#################################################################</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class=""><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">------------- EXCEPTION: Bio::Root::Exception -------------</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">MSG: Must have defined a valid name for Hit</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Error::throw</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl5/Bio/Search/Hit/GenericHit.pm:149</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Hit::PhatHit::Base::new maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:127</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Hit::PhatHit::blastx::new maker/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://blastx.pm:125/" target="_blank" class="">blastx.pm:125</a></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Hit::HitFactory::create /usr/local/share/perl5/Bio/Search/Hit/HitFactory.pm:124</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Factory::ObjectFactoryI::create_object /usr/local/share/perl5/Bio/Factory/ObjectFactoryI.pm:114</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Iteration::GenericIteration::newhits_below_threshold /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:506</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Iteration::GenericIteration::newhits /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:488</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Iteration::GenericIteration::hits /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:469</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Result::BlastResult::hits /usr/local/share/perl5/Bio/Search/Result/BlastResult.pm:168</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Bio::Search::Result::BlastResult::num_hits /usr/local/share/perl5/Bio/Search/Result/BlastResult.pm:242</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Widget::blastx::keepers</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/Widget/<a href="http://blastx.pm:164/" target="_blank" class="">blastx.pm:164</a></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Widget::blastx::parse</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/Widget/<a href="http://blastx.pm:132/" target="_blank" class="">blastx.pm:132</a></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: GI::blastx_as_chunks</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/GI.pm:2457</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: GI::blastx_as_chunks</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/GI.pm:2466</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Process::MpiChunk::_go</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/Process/MpiChunk.pm:2687</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Process::MpiChunk::run</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/Process/MpiChunk.pm:341</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Process::MpiChunk::run_all</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">maker/bin/../lib/Process/MpiChunk.pm:357</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Process::MpiTiers::run_all maker/bin/../lib/Process/MpiTiers.pm:287</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: Process::MpiTiers::run_all maker/bin/../lib/Process/MpiTiers.pm:287</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">STACK: maker/bin/maker:686</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">-----------------------------------------------------------</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">--> rank=NA, hostname=gena2</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">--> rank=NA, hostname=gena2</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">--> rank=NA, hostname=gena2</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">--> rank=NA, hostname=gena2</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">ERROR: Failed while doing blastx of proteins</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">ERROR: Chunk failed at level:8, tier_type:3</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">FAILED CONTIG:Contig1</span></p><div style="margin-bottom: 0.0001pt;" class=""><span style="font-family:'Courier New'" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">ERROR: Chunk failed at level:4, tier_type:0</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">FAILED CONTIG:Contig1</span></p><div style="margin-bottom: 0.0001pt;" class=""><span style="font-family:'Courier New'" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">examining contents of the fasta file and run log</span></p><div style="margin-bottom: 0.0001pt;" class=""><span style="font-family:'Courier New'" class=""> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class="">###########################################################</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-family:'Courier New'" class=""><br class=""></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><font face="Courier New" class="">Is anyone has any idea on this? </font></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><font face="Courier New" class=""><br class=""></font></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><font face="Courier New" class="">Thanks,</font></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><font face="Courier New" class="">SokLim</font></p></div></div>
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