[maker-devel] Failed while doing blastx of proteins

[Carson Holt]

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).

Thanks,
Carson



> On Oct 19, 2015, at 9:56 PM, Sok Lim Chew <14.chewsoklim at gmail.com> wrote:
> 
> Hi all,
> 
> 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.
> 
> #################################################################
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Must have defined a valid name for Hit
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486
> STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl5/Bio/Search/Hit/GenericHit.pm:149
> STACK: Bio::Search::Hit::PhatHit::Base::new maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:127
> STACK: Bio::Search::Hit::PhatHit::blastx::new maker/bin/../lib/Bio/Search/Hit/PhatHit/blastx.pm:125 <http://blastx.pm:125/>
> STACK: Bio::Search::Hit::HitFactory::create /usr/local/share/perl5/Bio/Search/Hit/HitFactory.pm:124
> STACK: Bio::Factory::ObjectFactoryI::create_object /usr/local/share/perl5/Bio/Factory/ObjectFactoryI.pm:114
> STACK: Bio::Search::Iteration::GenericIteration::newhits_below_threshold /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:506
> STACK: Bio::Search::Iteration::GenericIteration::newhits /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:488
> STACK: Bio::Search::Iteration::GenericIteration::hits /usr/local/share/perl5/Bio/Search/Iteration/GenericIteration.pm:469
> STACK: Bio::Search::Result::BlastResult::hits /usr/local/share/perl5/Bio/Search/Result/BlastResult.pm:168
> STACK: Bio::Search::Result::BlastResult::num_hits /usr/local/share/perl5/Bio/Search/Result/BlastResult.pm:242
> STACK: Widget::blastx::keepers
> maker/bin/../lib/Widget/blastx.pm:164 <http://blastx.pm:164/>
> STACK: Widget::blastx::parse
> maker/bin/../lib/Widget/blastx.pm:132 <http://blastx.pm:132/>
> STACK: GI::blastx_as_chunks
> maker/bin/../lib/GI.pm:2457
> STACK: GI::blastx_as_chunks
> maker/bin/../lib/GI.pm:2466
> STACK: Process::MpiChunk::_go
> maker/bin/../lib/Process/MpiChunk.pm:2687
> STACK: Process::MpiChunk::run
> maker/bin/../lib/Process/MpiChunk.pm:341
> STACK: Process::MpiChunk::run_all
> maker/bin/../lib/Process/MpiChunk.pm:357
> STACK: Process::MpiTiers::run_all maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: Process::MpiTiers::run_all maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: maker/bin/maker:686
> -----------------------------------------------------------
> --> rank=NA, hostname=gena2
> --> rank=NA, hostname=gena2
> --> rank=NA, hostname=gena2
> --> rank=NA, hostname=gena2
> ERROR: Failed while doing blastx of proteins
> ERROR: Chunk failed at level:8, tier_type:3
> FAILED CONTIG:Contig1
>  
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:Contig1
>  
> examining contents of the fasta file and run log
>  
> ###########################################################
> 
> Is anyone has any idea on this? 
> 
> Thanks,
> SokLim
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