[Bioperl-l] net blast not accommodated to the current NCBI?

[Guoneng Zhong]

Hi,

I am trying to send a remote Blast search and I get this error:

-------------------- EXCEPTION --------------------
MSG: Blast file tigre0og69F8_1.tblastx2.nr.temp.html is incomplete: 
can't find program name.
Possibly an unrecognized report format.

I looked at the html in question and it is the page you get on NCBI 
while you are waiting for the blast to complete.  When you submit a 
search on NCBI you don't get the search result immediately, but this "Be 
Patient" page.  After a few minutes you can click on the Format button 
and hope to get the result.  I was expecting the Blast.pm class to be 
doing that, waiting and waiting till it's ready.  Maybe I gave it the 
wrong param?  Here's my simple code:

use Bio::SeqIO;

my $format = "Fasta";
my $filename = $ARGV[0] || die "Need to know what file!";
my $sequence = Bio::SeqIO->new
(-file=>$filename,-format=>$format)->next_primary_
seq;
my @sequences = ($sequence);
my %runParams = (
         -method=>'remote',
         -prog=>'tblastx',
         -version=>2,
         -html=>0,
         -seqs=>[$sequence]
         );
my $blastObj = Bio::Tools::Blast->new(
                 -run => \%runParams,
                 -file=>'test.out',
                 -parse => 1,
                 -signif =>'1e-10',
                 -strict =>1
                 );


Thanks in advance for any help!

Oh, yes, I am aware of the example for remote blast, but reading it 
discouraged me from not writing my own blast search....

G