On Tue, Mar 13, 2012 at 1:35 PM, Robert Kern <robert.k...@gmail.com> wrote: > On 3/13/12 6:01 PM, ferreirafm wrote: >> Robert Kern-2 wrote >>> When you report a problem, you should copy-and-paste the output that you >>> got and >>> also state the output that you expected. I have no idea what you mean >>> when >>> you >>> say "subprocess.Popen seems not accept to run "qsub" over a second >>> program." >>> >> >> Code goes here: >> http://ompldr.org/vZDB5YQ >> >> stdout: >> $ no_name.py --toplist top_percent.list >> Traceback (most recent call last): >> File "/home6/psloliveira/ferreirafm/bin/no_name.py", line 73, in<module> >> main() >> File "/home6/psloliveira/ferreirafm/bin/no_name.py", line 68, in main >> comb_slt(toplist) >> File "/home6/psloliveira/ferreirafm/bin/no_name.py", line 55, in >> comb_slt >> subprocess.Popen([cmd, options], env=qsub_env) >> File "/share/apps/python/lib/python2.7/subprocess.py", line 679, in >> __init__ >> errread, errwrite) >> File "/share/apps/python/lib/python2.7/subprocess.py", line 1228, in >> _execute_child >> raise child_exception >> OSError: [Errno 13] Permission denied > > > You need to use a command list like this: > > ['qsub', 'combine_silent.linuxgccrelease', '-database', > '/home6/psloliveira/rosetta_database/', ...] > > The program to run ("qsub", not "qsub combine_silent.linuxgccrelease") and > each individual argument must be a separate string in the list. You cannot > combine them together with spaces. The reason you get a "Permission denied" > error is that it tried to find an executable file named "qsub > combine_silent.linuxgccrelease" and, obviously, could not.
See also the first "Note" box (and the description of "args" generally) under http://docs.python.org/library/subprocess.html#popen-constructor Cheers, Chris -- http://mail.python.org/mailman/listinfo/python-list
