If you are calling an interactive program, that would be expected behavior using system or backticks. There is no way to interact with a program through those APIs, so you're program just sits there waiting for input.
You can do a few things. You can pipe your answer to the program (if the program only expects 1 input) like so:
system("echo $input_file_name | $program");
If you're program asks multiple questions, then you will have to be more manual about it. You need to open a pipe to the program and print data to it, like you would a file. See open and the open tutorial
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