First, the 'cd' command can't be executed by Runtime.exec() in the first place (see How to use "cd" command using Java runtime?). You should be able to just set the working directory for the process when you call exec (see below).

Second, running 'cmd.exe /c' to execute your process isn't what you want here. You won't be able to get the results of your process running, because that is returned to the command window -- which eats the error and then closes without passing the error along to you.

Your exec command should look more like this:

CopyProcess p = Runtime.getRuntime().exec(
    command, null, "C:\Users\Eric\Documents\COSC\ecj");

Where 'command' looks like this:

CopyString command = "java ec.Evolve -file ec\app\tutorial5\tutorial5.params"

Edit: For reading error messages, try this:

CopyString error = "";
try (InputStream is = proc.getErrorStream()) {
    error = IOUtils.toString(is, "UTF-8");
}
int exit = proc.waitFor();
if (exit != 0) {
    System.out.println(error);
} else {
    System.out.println("Success!");
}

Here is the way to go:

Runtime rt = Runtime.getRuntime();
String[] commands = {"system.exe", "-get t"};
Process proc = rt.exec(commands);

BufferedReader stdInput = new BufferedReader(new 
     InputStreamReader(proc.getInputStream()));

BufferedReader stdError = new BufferedReader(new 
     InputStreamReader(proc.getErrorStream()));

// Read the output from the command
System.out.println("Here is the standard output of the command:\n");
String s = null;
while ((s = stdInput.readLine()) != null) {
    System.out.println(s);
}

// Read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
    System.out.println(s);
}

Read the Javadoc for more details here. ProcessBuilder would be a good choice to use.

You are not capturing STDERR, so when errors occur you do not receive them from STDOUT (which you are capturing). Try:

CopyBufferedReader input = new BufferedReader(new InputStreamReader(
               pr.getErrorStream()));