[Bioperl-l] Running Blast

[Lluis Armengol Dulcet]

Dear all, 

I am experiencing some problems while trying to blast a Bio::Seq object
against databases using Bio::Tools::Blast . I do not actually have any
clue, I've tried all imaginable combinations of passing sequences to the
Bio::Seq object but no matter what I try I always get the following
error report:


> -------------------- EXCEPTION --------------------
> MSG: Blast failed: No file created or a error occured upon submission.
> CONTEXT: Error in uNKNOWN CONTEXT
> SCRIPT: bioperl6.pl
> STACK:
> Bio::Tools::Blast::Run::Webblast::_blast(1165)
> Bio::Tools::Blast::Run::Webblast::blast_remote(572)
> Bio::Tools::Blast::_run_remote(1207)
> Bio::Tools::Blast::run(1138)
> Bio::Tools::SeqAnal::_initialize(264)
> Bio::Root::Object::new(448)
> main::bioperl6.pl(15)
> ---------------------------------------------------    

please find also enclosed the original script so you can take a look and
figure out what's going on ...

> #!/usr/local/bin/perl
>
> use Bio::Seq;
> use Bio::Tools::Blast;
>
> $seqObject = Bio::Seq->new( -file => '/root/Desktop/prova.tfa',
>		       -format => 'GenBank');
> %runParam = (
>                 -method   => 'remote',
>                  -prog     => 'blastn',
>                  -database => 'nr',
>                  -seqs     => [$seqObject],  # Bio::Seq.pm objects.
>                  );
>
>   $blastObj = Bio::Tools::Blast->new( -run     => \%runParam,
>                                        -parse   => 1,
>                                        -signif  => '1e-10',
>                                        -strict  => 1,
>                                        );

Thanks a lot for your help!

Lluís