While reading in output from Buffered Reader loop stalls when input is needed

I am making a program to automatically test a CLI. The one part that I am getting stuck at is reading in the output from the command line. My code looks like this:

private static File createTempScript(List<String> commands) throws IOException {
    final File tempScript = File.createTempFile("script", null);

    final Writer streamWriter = new OutputStreamWriter(new FileOutputStream(
            tempScript));
    final PrintWriter printWriter = new PrintWriter(streamWriter);

    for(String command: commands) {
        printWriter.println(command);
    }


    printWriter.close();

    return tempScript;
}

/**
 * Takes in a list of commands that then get sent to make a script. After the script is created this method will
 * then run the script.
 */
public void executeCommand(List<String> commands) throws IOException {

    final File tempScript = createTempScript(commands);

        final ProcessBuilder pb = new ProcessBuilder("bash", tempScript.toString());
        final Process process = pb.start();
        final BufferedReader in = new BufferedReader(new
                InputStreamReader(process.getInputStream()));
    final BufferedReader out = new BufferedReader(new
            InputStreamReader(process.getInputStream()));
        String s;
        while ((s = in.readLine()) != null) {
            if(!s.isEmpty())
            {
                Output.add(s);
            }
        }
}

The problem I am having now is that in the while loop whenever it gets to a line that I need to input in a command the program just hangs. Whenever I comment out that loop the program works fine.

Thanks for the help.