I am trying to run a remote blast using the Bio::Tools::Run::StandAloneBlastPlus but I think there is something wrong with my environment/installation. This is required for an assignment I am working on for school. I sent my code to my TA and she said that it worked. I am running OSX El Capitan. I don't have very much experience with programming so I'm not entirely sure how to troubleshoot.
My error is:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't find executable for 'blastdbcmd'; can't continue STACK: Error::throw STACK: Bio::Root::Root::throw /Library/Perl/5.18/Bio/Root/Root.pm:449 STACK: Bio::Tools::Run::WrapperBase::_run /Library/Perl/5.18/Bio/Tools/Run/WrapperBase/CommandExts.pm:974 STACK: Bio::Tools::Run::StandAloneBlastPlus::check_db /Library/Perl/5.18/Bio/Tools/Run/StandAloneBlastPlus.pm:1099 STACK: /Library/Perl/5.18/Bio/Tools/Run/StandAloneBlastPlus.pm:587
My code is (I don't think there are any problems here?):
my $fac = Bio::Tools::Run::StandAloneBlastPlus->new( -db_name => 'nt', -remote => 1 ); my $result = $fac->blastn(-query => 'infile.fa', -outfile => 'outfile.bls', -method_args => [ -num_alignments => 10 ] );