Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code is right, the script should output the query name and the hit name in terminal. Although the script doesn't throw out any errors when I run it from command line, I don't get any output. I've let the program run for hours and still nothing. I'm using BioPerl-1.6.1 and Perl-5.16.1 on Ubuntu 12.04 LTS. Any help would be appreciated.

Here's the script:

#!/home/mack/bin/perl
use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;


my $prog='blastn';
my $db='nr';
my $e_val='1e-10';
my $Input='diffexp1';
my @params = ('-prog' =>  $prog, '-data' =>  $db, '-expect' =>
$e_val, '-readmethod' => 'SearchIO');

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

$r =$factory->submit_blast($Input);
while (@rids =$factory->each_rid ){
    for $rid (@rids ){
      $rc =$factory->retrieve_blast($rid);
   }
}

my $report = Bio::SearchIO->new(-file =>$rc, -format =>'blast');
while (my $result = $report->next_result) {
    my $i=0;
    while (my $hit = $result->next_hit){
    print STDOUT $result->query_name, "\t";
    print STDOUT $hit->name, "\t";
    }
}
    if (i==0) {print STDOUT "No Hits \n"; }