But then also javascript code not running.

Still just a html question

still s browser like firefox will tell you what is wrong

as would webserver logs

You're still not "calling javascript from your CGI," and the sooner you stop referring to it that way, the sooner you might be able to understand the real problem. Your CGI prints an HTML page which (if it works as you intend) includes a link to a javascript file and a click event tied to a DOM element. It's up to your browser -- not the CGI -- to put all that together and "call" things when you click. If your clicking doesn't get the results you want, inspect your HTML and see if it has the code you expect, and use a tool like Firebug or Chrome's Developer Tools to look for javascript errors when you click. Trying to fix the CGI is starting at the wrong end; start at the client where the problem is.

Also, try to pull up the javascript link directly in your browser. My first guess, since you say the javascript is produced by a perl script in the same directory as the CGI (which may not be wrong, but is certainly unusual), is that you have a server configuration problem -- the server isn't configured to execute .js files as a CGI, for example -- so you'll see the perl source instead of its javascript output, or get a permissions error. But it could be many different things.