The usual way to deal with something like this is to wrap your system call in an eval block, and use an alarm to set a timeout. For example:

my $timeout = 20;   # or whatever is appropriate

eval {
    local $SIG{ALRM} = sub { die "timedout" };
    alarm $timeout;
    # Your system call goes here....
    alarm 0;
};

if ($@) {
    #  $@ will contain error message, if any
}
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Hope this helps,
Darren :)