The method "query_name" will not run because $result is undefined when I use Dumper. I thought I accounted for this in my first "if" statement where if "0" is returned, then it's supposed to wait 5 seconds and check the server again for a result. I can't seem to figure out exactly where the problem is. Here is the script: 
#loop over rids to check server for a result
        foreach my $rid (@rids) {
            my $blast_results = $blast_factory -> retrieve_blast($rid)
+;

            if ($blast_results == 0) { #still waiting to complete sear
+ch
                print STDERR "."; #watch dots while waiting
                sleep 5; #pause between checking for results
            }
            elsif ($blast_results == (-1)) {#error returned, remove RI
+D from stack
                print STDERR "retrieve_blast returns -1\n";
                $blast_factory -> remove_rid($rid);
            }

            #use Bio::SearchIO to return a Bio::SearchIO result object
            else {
                print "Receiving blast results...\n";
                my $result = $blast_results -> next_result();
                print Dumper ($result);
                my $filename = $result -> query_name()."\.out";
                $blast_factory -> save_output ($filename);
                $blast_factory -> remove_rid($rid);

[download]
Can anyone see the problem?

In reply to undefined value returned by terriblue

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