title: subprocess not catching stdout
body: <p>im trying since days to figure out why my subprocess.Popen does not catch the stdout. Maybe it has something to do with the fact that the subprocess outputs a file. I found this out when I run a subprocess without an output file and the stdout (that you would see at the terminal) was cought. Can you please help me how to catch it in the scenario with the output file, so I dont want to catch the output from the file but only the terminal output, so running output. Any kind of help is very appreciated.</p>
  <pre><code>     command = &quot;cnvkit.py call %s -o %s&quot; % (file, output)
       process_call = subprocess.Popen(command.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=sfs.path('cnv_app/call_CNS/'), universal_newlines=True)
  stdout, stderr = process_call.communicate()
       if process_call.returncode and stderr:
            output_call = stdout
            output_err_call = stderr
       else:
            output_call = stdout 
            process_call.poll()
            response = {'output_call': output_call, 'output_err_call': output_err_call}
  </code></pre>