On Oct 7, 2014 11:46 AM, "Ulf Schaefer" <Ulf.Schaefer@phe.gov.uk> wrote:

Dear all

Maybe one of you can shed some light on this error message that I see in
the log file for one of my handler processes. I get about one of them
per second. The effect is that most of the jobs remain in the "waiting
to run" stage.

The postgres database is running on a separate server and appear to be
doing just fine.

Any help is greatly appreciated.

Thanks
Ulf

---

galaxy.jobs.handler ERROR 2014-10-07 10:32:24,676 Exception in monitor_step
Traceback (most recent call last):
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py",
line 161, in __monitor
     self.__monitor_step()
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py",
line 184, in __monitor_step
     hda_not_ready =
self.sa_session.query(model.Job.id).enable_eagerloads(False) \
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do
     return getattr(self.registry(), name)(*args, **kwargs)
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1088, in query
     return self._query_cls(entities, self, **kwargs)
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 108, in __init__
     self._set_entities(entities)
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 117, in _set_entities
     self._setup_aliasizers(self._entities)
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 132, in _setup_aliasizers
     _entity_info(entity)
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/util.py",
line 578, in _entity_info
     mapperlib.configure_mappers()
   File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py",
line 2260, in configure_mappers
     raise e
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers.  Original exception was:
When initializing mapper Mapper|Queue|kombu_queue, expression 'Message'
failed to locate a name ("name 'Message' is not defined"). If this is a
class name, consider adding this relationship() to the <class
'kombu.transport.sqlalchemy.Queue'> class after both dependent classes
have been defined.

---

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