pm production run crash when job exists in slurm #195
Description
If a job is running in slurm when doing pm production run, the script crashes with the following output:
'''2013-02-20 11:55 (INFO): Running analysis defined by config file /proj/a2010002/nobackup/illumina/M.Uhlen_12_06/P282_137C_index5/130213_BH07P4ADXX/P282_137C_index5-bcbb-config.yaml
2013-02-20 11:55 (INFO): job is queued and active
2013-02-20 11:55 (WARNING): job is queued and active; please terminate job before proceeding
2013-02-20 11:55 (WARNING): Not running job
2013-02-20 11:55 (INFO): Running analysis defined by config file /proj/a2010002/nobackup/illumina/M.Uhlen_12_06/P282_116B_index11/130213_BH07P4ADXX/P282_116B_index11-bcbb-config.yaml
Traceback (most recent call last):
File "/bubo/home/h27/funk_001/.virtualenvs/master/bin/pm", line 5, in
pkg_resources.run_script('scilifelab==0.3.0dev', 'pm')
File "/bubo/home/h27/funk_001/.venvburrito/lib/python/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/bubo/home/h27/funk_001/.venvburrito/lib/python/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script
execfile(script_filename, namespace, namespace)
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/EGG-INFO/scripts/pm", line 46, in
app.run()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/cement-2.0.2-py2.7.egg/cement/core/foundation.py", line 451, in run
self.controller._dispatch()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/core/controller.py", line 52, in _dispatch
getattr(self, func['label'])()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/core/bcbio.py", line 90, in run
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/ext/ext_distributed.py", line 73, in monitor
return self._monitor_job(idfile, **{'workingDirectory':work_dir})
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/ext/ext_distributed.py", line 98, in _monitor_job
s.initialize()
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/init.py", line 274, in initialize
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/wrappers.py", line 59, in init
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/errors.py", line 90, in error_check
drmaa.errors.AlreadyActiveSessionException: code 11: DRMAA session already exist.'''