Most likely you just need to close(STDOUT) in the child process. See this node: CGI and Background Processes.

In your case I would do this:

use IPC::Open2;

my @cmd = ('/var/www/cgi-bin/nuScore/ProcessLongData.pl',
             $DirName, $maxSeqLen, $minSeqLen, $WindowSize, $Email);
open(NULL, "+</dev/null");
my $pid = open2(">&NULL", "<&NULL", @cmd);
...
[download]

This is much, much safer since the parameters for your script, $DirName, $maxSeqLen, etc. are coming directly from your CGI parameters.