In the example you linked to -- you're giving a relative path.
Without knowing how you're calling the program (CGI? cron?), I'd assume it's just an issue with a current working directory that's not the same as your script. (this is quite common for perl modules -- you'll want to work relative to __FILE__, or some other similar trick)
But, without code, the error messages, or more info about the calling context, any help you get is going to be pure speculation.
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