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<div class="">Agreed. It would be nice to know whether this is a Bioperl bug that needs addressing, but I’m not sure how easy it would be to pull out a test case.</div>
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<div class="">chris</div>
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<div class="">On Oct 20, 2015, at 10:52 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div>
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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).
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<div class="">Thanks,</div>
<div class="">Carson</div>
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<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>
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<div dir="ltr" class=""><span style="font-size:12.8px" class="">Hi all,</span>
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<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>
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<div style="font-size:12.8px" class="">#################################################################</div>
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<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="https://urldefense.proofpoint.com/v2/url?u=http-3A__blastx.pm-3A125_&d=BQMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=fqGWJ56-muW3FBKC6Cbz3rMR9_EKol7EF4l2eG4sGAg&s=PSb1aTjH8qAn1bdZOkMuITnoAiAzHnWS0M8ufebekQI&e=" 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="https://urldefense.proofpoint.com/v2/url?u=http-3A__blastx.pm-3A164_&d=BQMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=fqGWJ56-muW3FBKC6Cbz3rMR9_EKol7EF4l2eG4sGAg&s=ZDnzZ79a2Dv2BtNxEli8n7esCMpdbJwFAry1gbkpTl4&e=" 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="https://urldefense.proofpoint.com/v2/url?u=http-3A__blastx.pm-3A132_&d=BQMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=fqGWJ56-muW3FBKC6Cbz3rMR9_EKol7EF4l2eG4sGAg&s=PIoSP65wFizG2H4U-z9JExhm1rLXiZgCO6CkQ7W1E80&e=" 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">
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<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">
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<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">
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<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="">
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<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>
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