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.
--
Robert Kern
"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco
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