Java APIs

Ok, here's the problem:

I run a perl script in java using the Runtime.exec(String command) method, I hand this process to a thread which gets the InputStream from the process, and reads it byte by byte. Each time it reads a byte I immediately write that byte to the file in a syncronized block of code. Meanwhile, outside of this thread I wait until the process completes execution using the Process waitFor() method, then I close the output stream I was using for writing to the file.

This does not work properly and I can not figure out why. It usually only finishes writing out half or less than half the file until I get an error reading Bad File Descriptor. Here is the error and the code, any suggestions as to why this doesn't work would be greatly appriciated...

java.io.IOException: Bad file descriptor
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:260)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:66)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:79)
at edu.utexas.arlut.spars.libs.util.ProcessOutFile$InputStreamFile.run(ProcessOutFile.java:60)

public class ProcessOutFile
{
private InputStreamFile m_std;
private InputStreamFile m_err;


public ProcessOutFile(Process proc, BufferedOutputStream out)
{
m_std = new InputStreamFile(new BufferedInputStream(proc.getInputStream()), out);

m_std.start();

try {
proc.waitFor();
out.close();
} catch ( Exception e ) {
e.printStackTrace();
}
}

class InputStreamFile extends Thread {
private final BufferedInputStream m_in;
private BufferedOutputStream out;
StringBuffer tempBuffer = new StringBuffer();

public InputStreamFile(BufferedInputStream in, BufferedOutputStream out)
{
m_in = in;
this.out = out;
}

public void run()
{
int nextByte;

try
{
while (true)
{
nextByte = m_in.read();

if (nextByte == -1)
{
break;
}

synchronized (this)
{

out.write((char)nextByte); // Line 60
}
}
}
catch (Exception e)
{
e.printStackTrace();
}
}
}
}