I'm having a problem nailing down a problem trying to send a query to a web server and retrieving the results. I'm working with the Bio::Tools::Run::RemoteBlast bioperl module.

This is the portion of script where I believe the problem is coming from:

#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');

#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";

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

#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 $blast_results == (-1);
}
#if result, use Bio::SearchIO to return Bio::SeqIO result object
if ( ref($blast_results)) {
print "Receiving blast results...\n";
my $result = $blast_results -> next_result();
$blast_factory -> remove_rid($rid); #remove rid from stack

[download]


The error message I get is this:

Blasting sequence number 1
-----WARNING-----
MSG:
-----------------------
retrieve_blast returns -1

Any ideas?

In reply to Problem retrieving results from web server by terriblue

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