my $thr  = threads->create( sub {
    my $threadId = $i;

    open my $REFERENCE_FILE, '<', "$refFileName" or 
        die "Can't open $refFileName: $!";

    while ( defined( my $item = $inQ->dequeue() ) )
    {
        my $lot          = $item->{ 'lot'   };
        my $batch        = $item->{ 'batch' };
        my $part         = $item->{ 'part'  };
        my $fastaComment = $item->{ 'fasta' };
        my $readSequence = $item->{ 'read'  };
        
        my @hits   = split /[,]/, $fastaComment;
        my $beadID = shift( @hits );
        
        # do some sutff to the current item that makes use of
        # REFERENCE_FILE
        my $bestSeedOverallMismatches = $INF;
        my @bestSeedExtensions        = ();
        foreach my $hitString ( @hits )
        {
            ...
        }
        
        my %result = ( 'lot'        => $lot,
                       'batch'      => $batch,
                       'part'       => $part,
                       'thread'     => $threadId,
                       'extensions' => \@bestSeedExtensions,
                       'num_mm'     => $bestSeedOverallMismatches,
                       'beadid'     => $beadID,
                       'read'       => $readSequence, );
        
        $outQ->enqueue( \%result );
    }

    close $REFERENCE_FILE;
} );#end sub