You should really look at Process Builder. It is really built for this kind of thing.

ProcessBuilder pb = new ProcessBuilder("myshellScript.sh", "myArg1", "myArg2");
 Map<String, String> env = pb.environment();
 env.put("VAR1", "myValue");
 env.remove("OTHERVAR");
 env.put("VAR2", env.get("VAR1") + "suffix");
 pb.directory(new File("myDir"));
 Process p = pb.start();

You could use Runtime.exec(). Here is a very simple example:

import java.io.*;
import java.util.*;

class Foo {
    public static void main(String[] args) throws Exception {
        // Run command and wait till it's done
        Process p = Runtime.getRuntime().exec("ping -n 3 www.google.de");
        p.waitFor();

        // Grab output and print to display
        BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));

        String line = "";
        while ((line = reader.readLine()) != null) {
            System.out.println(line);
        }
    }
}

Your code is right and I am sure you are not getting exceptions, if you read using proc.getErrorStream() you will not get anything.
Commands 100% get executed that way, having said that now thing is that you are echo'ing something and you need to read it back using BufferedReader.

Check below example which will successfully create a directory called "stackOverflow" and print what you are echo'ing. For the putting it into a log file I am afraid that you can do it using ">", you may have to use some editor command or create file using Java.

Bottom line: Runtime.getRuntime().exec("command") is the correct and defined way to execute Unix commands or scripts from Java and it WORKS.

test.sh

#!/bin/bash
echo "hola"
mkdir stackOverflow

Test.java

import java.io.*;
public class Test {

        public static void main(String[] args) throws Exception {
                try {
                        String target = new String("/home/hagrawal/test.sh");
// String target = new String("mkdir stackOver");
                        Runtime rt = Runtime.getRuntime();
                        Process proc = rt.exec(target);
                        proc.waitFor();
                        StringBuffer output = new StringBuffer();
                        BufferedReader reader = new BufferedReader(new InputStreamReader(proc.getInputStream()));
                        String line = "";                       
                        while ((line = reader.readLine())!= null) {
                                output.append(line + "\n");
                        }
                        System.out.println("### " + output);
                } catch (Throwable t) {
                        t.printStackTrace();
                }
        }
}

This is a simple code to execute the shell script and read its output:

import java.io.*;                                                            

public class Test {                                                          
  public static void main(String[] args) throws Exception {                  
    String[] command = { "./flows.sh", "suspend" };         
    Process process = Runtime.getRuntime().exec(command);                    
    BufferedReader reader = new BufferedReader(new InputStreamReader(    
        process.getInputStream()));                                          
    String s;                                                                
    while ((s = reader.readLine()) != null) {                                
      System.out.println("Script output: " + s); // Replace this line with the code to print the result to file                     
    }                                                                        
  }                                                                          
}      

To print it to a file, just replace the System.out.println for the code to write into a file

You need Runtime.getRuntime().exec(...). See a very extensive example (don't forget to read the first three pages).

Keep in mind that Runtime.exec is not a shell; if you wish to execute a shell script your command line would look like

/bin/bash scriptname

That is, the shell binary you need is fully qualified (although I suspect that /bin is always in the path). You can not assume that if

myshell> foo.sh

runs,

Runtime.getRuntime.exec("foo.sh");

also runs as you are already in a running shell in the first example, but not in the Runtime.exec.

A tested example (Works on My Linux Machine(TM)), mosly cut-and-past from the previously mentioned article:

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
public class ShellScriptExecutor {

    static class StreamGobbler extends Thread {
        InputStream is;

        String type;

        StreamGobbler(InputStream is, String type) {
            this.is = is;
            this.type = type;
        }

        public void run() {
            try {
                InputStreamReader isr = new InputStreamReader(is);
                BufferedReader br = new BufferedReader(isr);
                String line = null;
                while ((line = br.readLine()) != null)
                    System.out.println(type + ">" + line);
            } catch (IOException ioe) {
                ioe.printStackTrace();
            }
        }
    }


    public static void main(String[] args) {
        if (args.length < 1) {
            System.out.println("USAGE: java ShellScriptExecutor script");
            System.exit(1);
        }

        try {
            String osName = System.getProperty("os.name");
            String[] cmd = new String[2];
            cmd[0] = "/bin/sh"; // should exist on all POSIX systems
            cmd[1] = args[0];

            Runtime rt = Runtime.getRuntime();
            System.out.println("Execing " + cmd[0] + " " + cmd[1] );
            Process proc = rt.exec(cmd);
            // any error message?
            StreamGobbler errorGobbler = new StreamGobbler(proc
                    .getErrorStream(), "ERROR");

            // any output?
            StreamGobbler outputGobbler = new StreamGobbler(proc
                    .getInputStream(), "OUTPUT");

            // kick them off
            errorGobbler.start();
            outputGobbler.start();

            // any error???
            int exitVal = proc.waitFor();
            System.out.println("ExitValue: " + exitVal);
        } catch (Throwable t) {
            t.printStackTrace();
        }
    }
}