Exit code 137 (128+9) indicates that your program exited due to receiving signal 9, which is SIGKILL. This also explains the killed message. The question is, why did you receive that signal?
The most likely reason is probably that your process crossed some limit in the amount of system resources that you are allowed to use. Depending on your OS and configuration, this could mean you had too many open files, used too much filesytem space or something else. The most likely is that your program was using too much memory. Rather than risking things breaking when memory allocations started failing, the system sent a kill signal to the process that was using too much memory.
As I commented earlier, one reason you might hit a memory limit after printing finished counting is that your call to counter.items() in your final loop allocates a list that contains all the keys and values from your dictionary. If your dictionary had a lot of data, this might be a very big list. A possible solution would be to use counter.iteritems() which is a generator. Rather than returning all the items in a list, it lets you iterate over them with much less memory usage.
So, I'd suggest trying this, as your final loop:
for key, value in counter.iteritems():
writer.writerow([key, value])
Note that in Python 3, items returns a "dictionary view" object which does not have the same overhead as Python 2's version. It replaces iteritems, so if you later upgrade Python versions, you'll end up changing the loop back to the way it was.