Note that we're reading the process output line by line into our StringBuilder. Due to the try-with-resources statement we don't need to close the stream manually. The ProcessBuilder class let's us submit the program name and the number of arguments to its constructor.

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

public class ProcessOutputExample
{
    public static void main(String[] arguments) throws IOException,
            InterruptedException
    {
        System.out.println(getProcessOutput());
    }

    public static String getProcessOutput() throws IOException, InterruptedException
    {
        ProcessBuilder processBuilder = new ProcessBuilder("java",
                "-version");

        processBuilder.redirectErrorStream(true);

        Process process = processBuilder.start();
        StringBuilder processOutput = new StringBuilder();

        try (BufferedReader processOutputReader = new BufferedReader(
                new InputStreamReader(process.getInputStream()));)
        {
            String readLine;

            while ((readLine = processOutputReader.readLine()) != null)
            {
                processOutput.append(readLine + System.lineSeparator());
            }

            process.waitFor();
        }

        return processOutput.toString().trim();
    }
}

Prints:

java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

I've often written something like:

class StreamHandler extends Thread {

    InputStream is;
    Writer writer;

    StreamHandler(InputStream is, Writer writer) {
        super("StreamHandler");

        this.is = is;
        this.writer = writer;
    }

    @Override
    public void run() {
        try (InputStreamReader isr = new InputStreamReader(is)) {

            char buffer[] = new char[256];
            int n;
            while ((n = isr.read(buffer)) > 0) {
                writer.write(buffer, 0, n);
            }
        } catch (IOException e) {
            System.err.println("StreamHandler: " + e);
        }
    }
}

While I've used this for capturing the output stream to my own buffer, you could simply echo to stdout in real time like:

Process process = Runtime.getRuntime().exec(...);
Writer writer = new OutputStreamWriter(System.out);
StreamHandler stdout_handler = new StreamHandler(process.getInputStream(), writer);
stdout_handler.start();

You're deadlocked for 5 hours waiting for the process to exit while it is waiting for you to consume some input so it won't be blocked producing it so it can exit.

You should consume the input first, and then do the waitFor().

NB You also need to close the output stream to the process so it isn't waiting for input.

I believe this is what you're looking for:

  String line;
  Process p = Runtime.getRuntime().exec(...);
  BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
  while ((line = input.readLine()) != null) {
    System.out.println(line);
  }
  input.close();

A quicker way is this:

public static String execCmd(String cmd) throws java.io.IOException {
    java.util.Scanner s = new java.util.Scanner(Runtime.getRuntime().exec(cmd).getInputStream()).useDelimiter("\\A");
    return s.hasNext() ? s.next() : "";
}

Which is basically a condensed version of this:

public static String execCmd(String cmd) throws java.io.IOException {
    Process proc = Runtime.getRuntime().exec(cmd);
    java.io.InputStream is = proc.getInputStream();
    java.util.Scanner s = new java.util.Scanner(is).useDelimiter("\\A");
    String val = "";
    if (s.hasNext()) {
        val = s.next();
    }
    else {
        val = "";
    }
    return val;
}

I know this question is old but I am posting this answer because I think this may be quicker.

Edit (For Java 7 and above)

Need to close Streams and Scanners. Using AutoCloseable for neat code:

public static String execCmd(String cmd) {
    String result = null;
    try (InputStream inputStream = Runtime.getRuntime().exec(cmd).getInputStream();
            Scanner s = new Scanner(inputStream).useDelimiter("\\A")) {
        result = s.hasNext() ? s.next() : null;
    } catch (IOException e) {
        e.printStackTrace();
    }
    return result;
}

Use Apache Commons Exec, it will make your life much easier. Check the tutorials for information about basic usage. To read the command line output after obtaining an executor object (probably DefaultExecutor), create an OutputStream to whatever stream you wish (i.e a FileOutputStream instance may be, or System.out), and:

executor.setStreamHandler(new PumpStreamHandler(yourOutputStream));