proccessFiles = os.popen('/bin/bunzip2 -cd ' + fileInput + ' > ' + self.file_out)
This line is non-blocking. Therefore it will start the command, but the few following lines are already reading the file. This is basically a concurrency issue. Try to wait for the command to complete before reading the file.
Also see:
Python popen command. Wait until the command is finished since os.popen
is deprecated since python-2.6 (depending on which version you are using).
Sidenote - The same happens to the line below. The file may, or may not, exist after executing the following line:
os.popen('touch ' + self.file_out)