If you don't need it to work on Windows, use Net::OpenSSH:

my $ssh = Net::OpenSSH->new($SERVER,
                            user => $USER,
                            master_opts => [-i => $KEYFILE],
                            master_stderr_discard => 1);
$ssh->error and die "unable to connect to remote host: " . $ssh->error
+;

my $out = $ssh->capture({stdin_data => $lines});
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