[maker-devel] Failed while doing blastx of proteins

[Fields, Christopher J]

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.

chris

On Oct 20, 2015, at 10:52 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

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<mailto: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<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=>
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<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=>
STACK: Widget::blastx::parse
maker/bin/../lib/Widget/blastx.pm:132<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=>
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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