[Bioperl-l] Problems using Bio::Tools::Blast

[Steve Chervitz]

Yes, this is an erroneous exception that you don't need to worry
about when using the NCBI server. It's a holdover from the days
when the server returned the actual blast report. The Blast
object still expects this to be the case.

If you use the run_blast_remote.pl script in the examples/blast
directory of the distribution, it catches this exception and
informs you that you can fetch the report using the handy
retrieve_blast.pl script (also in examples/blast).

FYI, the actual exception handling code is in the create_blast()
function of blast_config.pl, which is required by
run_blast_remote.pl.

Steve

gert thijs wrote:

> gert thijs wrote:
> >
> >
> > This script returns the following exception:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: Blast file gi_609339_gb_U18675.blastn2.nr.temp.html is
> incomplete: can't
> > find program name.
> > Possibly an unrecognized report format.
> > CONTEXT: Error in uNKNOWN CONTEXT
> > SCRIPT: ./ParseBlastReport2.pl
> > STACK:
> > Bio::Tools::Blast::Run::Webblast::_blast(1175)
> > Bio::Tools::Blast::Run::Webblast::blast_remote(580)
> > Bio::Tools::Blast::_run_remote(1244)
> > Bio::Tools::Blast::run(1178)
> > Bio::Tools::SeqAnal::_initialize(279)
> > Bio::Root::Object::new(462)
> > main::./ParseBlastReport2.pl(33)
> > ---------------------------------------------------
>
> I have been looking at the all the intermediate file, referred
> to in the
> message, and it seems to me that the error is not produced
> while processing
> the results but while reading the page returned by the ncbi
> queueing system.
> Scrolling through the code of
> Bio::Tools::Blast::Run::webbblast.pm I saw that
> the error message is produced while searching for the text
> 'BLAST[NPX]\s'. But
> this line isn't in the intermediate queueing files.
> I have attached this intermediate files to this mail.
>
> Gert
>