So, where is the problem?

Is the problem that $ARGV[0] is set up in the wrong way? Then the problem is not within Perl but how you call your program. Please review Re: How to pass command line arguments with file names containing spaces and Re: How to pass command line arguments with file names containing spaces, which address this situation.

Is the problem that the program you are calling (mer) does not receive the parameters correctly? Then you need to compare how you start the program manually to how you start it from Perl.