I would say, make a wrapper script around the long running commands that gives a feedback while doing the long running jobs. Like printing a '@' (or something else that can't occur in the output of the command itself) every second.

The wrapper script could fork a second process (or thread) which executes the long running command, while the main process in a loop sleeps one second, prints a '@' and then does a non-blocking check whether the child finished already.

For non-blocking waits see 'perldoc -f waitpid', but there are also some excellent modules that take care of the forking/threading/signaling or the forked process could simply create a file as signal that it has finished.