[Bioperl-l] StandAloneBlast.pm and RemoteBlast.pm

Jason Stajich jason at cgt.duhs.duke.edu
Thu Jul 22 16:28:58 EDT 2004

They work fine with all NCBI blastall T?BLAST[XPN].

Are you sure your databases were formatted with
% formatdb -i est -p F

Are you sure your index files for the database are in that directory.
Does a commandline blast of tblastn against this est db work without
invoking bioperl at all.  There is nothing magic in standaloneblast - it
is just setting commandline arguments to blastall for you.

Add the parameter -verbose => 1 and you will see the command-line that is
being executed by perl.  Check that it is consistent with what you expect
it be saying.


On Thu, 22 Jul 2004 jwon at ucalgary.ca wrote:

> Hi,
> I am trying to use StandAloneBlast.pm and RemoteBlast.pm to automate BLASTing
> of several sequences that I am interested in.  I need to use the 'tblastn'
> program against the 'est' database.  However, when i set the parameters for
> the StandAloneBlast.pm and RemoteBlast.pm, I code:
> my @params = ('program'=>'tblastn', 'database'=>'est', _READMETHOD=>"Blast")
> my $f = Bio::Tools::Run::StandAloneBlast->new(@params);
> $f->outfile('blast.out');
> my $blast_report = $f->blastall($sequence);
> but after execution, it tells me:
> [blastall] WARNING: gi|11499797|ref|NP_071040.1|: Could not find index files
> for database /a1000/formatted_dbs/genbanknr/est
> ------------- EXCEPTION --------------
> MSG: blastall call crashed:
> when i run the same program with the database parameter set to "swissprot,
> and program set to "blastp", the program works fine.
> Do these objects not work with the tblastn program against the est database?
> Thank you in advance for your help.
> Jackson
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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