...
use Data::Dumper;
...
#create remote blast factory object and initialize blast parameters
my $blast_factory = Bio::Tools::Run::RemoteBlast -> new (    
    '-prog' => 'blastn',
    '-data' => 'nr',
    '-expect' => '1e-10',
    '-readmethod' => 'SearchIO');

print Dumper( $blast_factory );
#loop over all sequences input and count how many sequences are found
my $count = 0;
while (my $seq = $seqio -> next_seq) {
$count++;

#loop to blast each sequence against the database
my $job = $blast_factory -> submit_blast ($seq);
print "Blasting sequence number $count\n";
print Dumper( $job );
#loop to load rids returned for the blast job submitted
while (my @rids = $blast_factory -> each_rid) {

#loop over rids to check server for a result
foreach my $rid (@rids) {
print Dumper( $rid );
my $blast_results = $blast_factory -> retrieve_blast($rid);
print Dumper( $blast_results );
...
[download]

Thanks for the suggestion...much appreciated.

I've verified there's nothing wrong with the network and I've incorporated Data::Dumper so see what's going on:



my $blast_factory = Bio::Tools::Run::RemoteBlast -> new (    
'-prog' => 'blastn',
'-data' => 'nr',
'-expect' => '1e-10',
'-readmethod' => 'SearchIO');

print Dumper ($blast_factory); #ok

#loop over all sequences input and count how many sequences are found
my $count = 0;
while (my $seq = $seqio -> next_seq) {
$count++;

#loop to blast each sequence against the database
my $job = $blast_factory -> submit_blast ($seq);
print "Blasting sequence number $count\n";

print Dumper($job); #returns 1, ok

#loop to load rids returned for the blast job submitted
while (my @rids = $blast_factory -> each_rid) {

#loop over rids to check server for a result
foreach my $rid (@rids) {

print Dumper ($rid); #returns rid#, ok

my $blast_results = $blast_factory -> retrieve_blast($rid);

print Dumper ($blast_results); #returns -1, PROBLEM

#check to see if a result object is returned
if ( !ref($blast_results) ) { #if error returned remove rid from stack
if ($blast_results == 0) {
print STDERR "retrieve_blast returns 0\n"; #watch dots 
sleep 5; #pause between submitting requests to genbank server
}
elsif ($blast_results == (-1)) {
print STDERR "retrieve_blast returns -1\n";
$blast_factory -> remove_rid($rid);
}
last if $blast_results == (-1);
}
#if result, use Bio::SearchIO to return a Bio::SeqIO result object
if ( ref($blast_results)) {
print "Receiving blast results...\n";
my $result = $blast_results -> next_result();
$blast_factory -> remove_rid($rid); #remove rid from stack
[download]


This is the output:



$VAR1 = bless( {
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_readmethod' => 'SearchIO',
                 '_flush_on_write' => 1,
                 '_root_verbose' => 0
               }, 'Bio::Tools::Run::RemoteBlast' );
Blasting sequence number 1
$VAR1 = '1';
$VAR1 = '1080865802-2043-175938892824';

-------------------- WARNING ---------------------
MSG: 

---------------------------------------------------
$VAR1 = -1;
retrieve_blast returns -1
[download]

Looks like it's able to use the $blast_factory settings to obtain an rid# from the queue, but once it's done that, throws an error when trying to retrieve the result object.