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Nucleotide BLAST database './nt ' does not exist in the NCBI servers

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Aug 12th, 2010
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  1. Why do I get this error - "Nucleotide BLAST database './nt' does not exist in the NCBI servers" - when running the code below? The stack trace is pasted below the code. Thank you.
  2.  
  3. #!/usr/bin/perl -w
  4. use strict;
  5. use Bio::Tools::Run::StandAloneBlastPlus;
  6. use Bio::Seq;
  7.  
  8. my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(-db_name => 'nt', -remote => 1);
  9. my $seq_obj = Bio::Seq->new(-id  =>"test query", -seq =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
  10. my $result = $fac->blastn(-query => $seq_obj);
  11.  
  12.  
  13.  
  14.  
  15. ------------- EXCEPTION: Bio::Root::Exception -------------
  16. MSG: /usr/local/blast+/bin/blastn call crashed: There was a problem running /usr
  17. /local/blast+/bin/blastn : BLAST Database error: Nucleotide BLAST database './nt
  18. ' does not exist in the NCBI servers
  19.  
  20. STACK: Error::throw
  21. STACK: Bio::Root::Root::throw /home/lupey/downloads/bioperl/bioperl-live/Bio/Roo
  22. t/Root.pm:472
  23. STACK: Bio::Tools::Run::WrapperBase::_run /home/lupey/downloads/bioperl/bioperl-
  24. live/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
  25. STACK: Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD /home/lupey/downloads/biop
  26. erl/bioperl-run/lib/Bio/Tools/Run/StandAloneBlastPlus.pm:1303
  27. STACK: Bio::Tools::Run::StandAloneBlastPlus::run /home/lupey/downloads/bioperl/b
  28. ioperl-run/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:264
  29. STACK: Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD /home/lupey/downloads/biop
  30. erl/bioperl-run/lib/Bio/Tools/Run/StandAloneBlastPlus.pm:1301
  31. STACK: ./myblastplus.pl:10
  32. -----------------------------------------------------------
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