Bug #4889

Updated by Tim Pierce over 5 years ago

I ran the cufflinks tool: http://cole-trapnell-lab.github.io/cufflinks/manual/ and tools logs its own progress by creating a loading bar and updating that loading bar by the millisecond(?). I ran this job: qr1hi-8i9sb-ajgkcn4cuk4cntm and it last logged at the part before the loading bar would come up. The job then ran ad infinitum and I had to cancel it. (The job ran 20 minutes here: "qr1hi-8i9sb-pmu3ffh19dny625":http://crvr.se/qr1hi-8i9sb-pmu3ffh19dny625 qr1hi-8i9sb-pmu3ffh19dny625 using a --quiet flag)


Possible solution: use @communicate.Popen@ instead of @subprocess.call@. https://docs.python.org/2/library/subprocess.html#subprocess.call "Do not use stdout=PIPE or stderr=PIPE with this function as that can deadlock based on the child process output volume. Use Popen with the communicate() method when you need pipes."