Java Process Execution Hangs

Java Process Execution Hangs

Here is my workflow:
I get job from DB, I run a few tasks, I run an external program that reads
a file and produces another one (this usually takes under 10 seconds).
Here is the code:
Process p = Runtime.getRuntime().exec(prog, null, new File(path));
BufferedReader stdInput = new BufferedReader(new
InputStreamReader(p.getInputStream()));
BufferedReader stdError = new BufferedReader(new
InputStreamReader(p.getErrorStream()));
String s;
String errorString = "";
while((s = stdInput.readLine()) != null) {
if(s.toLowerCase().contains("error")) {
Log.writeLog("error: " + s);
errorString += s + "\r\n";
}
}
if(errorString.length() > 1) {
Emailer.email(name + "*" + errorString, "ERROR");
}
while((s = stdError.readLine()) != null) {
Log.writeLog("ERROR: " + s);
}
However, the snippet hanged. I control the server that the code runs on
through LogMeIn, once I logged in, the process unblocked (total running
time around 280 seconds) and continued. The process did not produce an
ERROR results. This happens from time to time more often than we would
like to. We do quite a bit of small IOs operation in the program and the
harddrive gets pretty full from time to time.
Any idea what could be happening?
Thanks!
EDIT: the server is a just a regular computer that is connected to
LogMeIn. My fear is that since it is a regular computer, it may powerdown
the CPU/hard drive when not in use (not sure the correct terminology).
This would somewhat explain why it would continue once I logged in to
LogMeIn and had access to a computer.
EDIT2: directly following the process, I run this. And this hangs for an
absurd amount of time as well (usually 5 seconds, took 200+ seconds).
private void cleanup(String path) {
File srcPath = new File(path);
File[] files = srcPath.listFiles();
if(files != null) {
for(File file : files) {
if(file.isDirectory()) {
cleanup(file.getAbsolutePath());
} else {
if(file.getAbsolutePath().endsWith(".original")) {
String fileName = file.getAbsolutePath().substring(0,
file.getAbsolutePath().lastIndexOf(".original"));
IO.delete(fileName);
if(!IO.renameFile(file.getAbsolutePath(), new
File(fileName).getAbsolutePath())) {
Log.writeLogSevere("Failed to rename file, this could
be a problem..." + fileName);
} else {
Log.writeLog("Restored: " + fileName);
}
}
}
}
}