Question: StandAloneBlastPlus: Can't find executable for 'blastdbcmd'
0
gravatar for gfm255
2.9 years ago by
gfm2550
gfm2550 wrote:

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 ] );
rna-seq blast bioperl • 1.1k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 2.9 years ago by gfm2550

Did you download the pre-compiled blast+ binaries for OS X? That bundle should have contained blastdbcmd. Did you move any files out of that folder?

ADD REPLYlink written 2.9 years ago by genomax65k

I think I have blastdbcmd, but not the ncbi databases? If i type "blastdbcmd" this is the output:

BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/Users/gillian::]

To clarify, I want to run my pipeline in Eclipse, not in the command line.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by gfm2550

NCBI databases can be downloaded from here: ftp://ftp.ncbi.nih.gov/blast/db/ You will need to get all nt* files. It would be a large download.

ADD REPLYlink written 2.9 years ago by genomax65k

Did you manage to sort out your issue? I have a similar problem when trying to use Bio::Tools::Run::Alignment::Blat module

ADD REPLYlink written 12 months ago by prishly0
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