Hi,
I'm a PhD student in Tsinghua University, Beijing.
I set up a local Galaxy, and import a bed file. I want
to sort all the rows by the the second column' value, "start position"
,in ascending order. It failed when executed in my local version,
however, it's OK to run on the Galaxy's public site. The system is Ubuntu 9.10,and the python version is 2.6.4. The bed file is about 150,000 lines.Is it the problem
of database or other? I am not using
any external database for the local galaxy.
Best,
Weilong Guo
The error message is as follow.
----------------------------------
Traceback (most recent call last):
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/lib/galaxy/jobs/runners/local.py", line 122, in run_job
job_wrapper.finish( stdout, stderr )
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/lib/galaxy/jobs/__init__.py", line 569, in finish
self.sa_session.flush()
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
self._flush(objects)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/!
sqlalchemy/orm/session.py", line 1434, in _flush
flush_context.execute()
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
UOWExecutor().execute(self, tasks)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 773, in execute_save_steps
self.execute_cyclical_dependencies(trans, task, False)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 789, in execute_cyclical_dependencies
self.execute(trans, [t], isdelete)
File "/home/guoweilong/GWL-galaxy/ga!
laxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sq
lalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
self.save_objects(trans, task)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
c = connection.execute(statement.values(value_params), params)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
return Connection.executors[c](self, object, multiparam!
s, params)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
return self.__execute_context(context)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e, conne!
ction_invalidated=is_disconnect)
ProgrammingError: (ProgrammingErro
r) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE history_dataset_association SET update_time=?, info=?, blurb=?, peek=? WHERE history_dataset_association.id = ?' ['2009-12-21 02:41:54.450928', 'sort: \xe5\xa4\x9a\xe5\xad\x97\xe7\xac\xa6\xe6\xa0\x87\xe7\xad\xbe\xe2\x80\x9c$\\t\xe2\x80\x9d\n', 'error', 'no peek', 7]