system(" some command >&file &");
wait;
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You are causing your external process to background and detach from your process group.

You can't really wait for it to end like that in a reliable way...

Instead, do this:

if( my $pid = fork ) {
    print "I am the parent pid ($$), and I'm going to wait for $pid to
+ exit.\n";
    my $kid;
    do {

     $kid = waitpid $pid, 0;

    } while $kid > 0;
    exit 0;

} else {
    exec(qw(ls -al /tmp)); die "hrm, exec() failed: $!";
}
[download]

Using a '&' in the system() call causes perl to fork a shell and asks the shell to fork a kid. Then the shell returns and perl completely looses track of the kids.

UPDATE: Also, I just noticed that you probably need some kind of redirection:

    # exec(qw(ls -al /tmp)); die ... blah
    open my $out, ">", "filename" or die $!;
    open my $in, "-|", qw(ls -al /tmp) or die $!;
    print $out $_ while <$in>;
    close $out;
    close $in;
[download]

-Paul