use threads;
use threads::shared;
use Thread::Queue;
...

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() ) )
    {
        # get info from the current item
        my $lot          = $item->{ 'lot'   };
        my $batch        = $item->{ 'batch' };
        my $part         = $item->{ 'part'  };
        ...
        
        # perform an operation on the item
        ...
        
        my %result = ( 'lot'        => $lot,
                       'batch'      => $batch,
                       'part'       => $part,
                       'thread'     => $threadId,
                       'extensions' => \@bestSeedExtensions,
                       'num_mm'     => $bestSeedOverallMismatches,
                       'beadid'     => $beadID,
                       'read'       => $readSequence, );
        
        $outQ->enqueue( \%result ); # <------ I AM BROKEN :(
    }
} );# end sub