So I have a python script that runs a loop in which it calls a program A through subprocess.Popen waits for its output, then saves the output and then calls it again and so
You are seperating your p.poll() and your p.kill() by 20 seconds. By then the process could have finished. I would suggest moving the time.sleep(20) call around so that you poll and kill happen in the same time frame, to avoid killing a dead process. Below is an example run in iPython showing a similar error when killing a completed process:
In [2]: import subprocess
In [3]: p = subprocess.Popen("dir")
In [4]: p.poll()
Out[4]: 0
In [5]: p.kill()
---------------------------------------------------------------------------
WindowsError Traceback (most recent call last)
C:\Users\---\<ipython console> in <module>()
C:\Python26\lib\subprocess.pyc in terminate(self)
947 """Terminates the process
948 """
--> 949 _subprocess.TerminateProcess(self._handle, 1)
950
951 kill = terminate
WindowsError: [Error 5] Access is denied
Even if you kill directly after a poll that shows the processes is running it can finish before the next line is executed. I would also suggest adding a try-catch block for this exception and if it occurs poll again to see if the process actually completed.