Hi Galaxy Community,
I have recently setup a small local instance of Galaxy and, when trying to replicate the quickie 15 (about 454 Mapping with Lastz) steps, but using real 454 data, got this error in the execution of the "Comparing two datasets" tool. Would anyone have any hint about how to solve it? Apparently, there was a similar report of this issue to the list (in March, 2012), but I could not find the answer for it.
Thanks, in advance, for any help or advice!
Antonio
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Traceback (most recent call last):
File "/home/acbellorib/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 133, in run_job
job_wrapper.finish( stdout, stderr )
File "/home/acbellorib/galaxy-dist/lib/galaxy/jobs/__init__.py", line 684, in finish
self.sa_session.flush()
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py", line 127, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1356, in flush
self._flush(objects)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py", line 1434, in _flush
flush_context.execute()
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
UOWExecutor().execute(self, tasks)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 773, in execute_save_steps
self.execute_cyclical_dependencies(trans, task, False)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 789, in execute_cyclical_dependencies
self.execute(trans, [t], isdelete)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
self.execute_save_steps(trans, task)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
self.save_objects(trans, task)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
c = connection.execute(statement.values(value_params), params)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 824, in execute
return Connection.executors[c](self, object, multiparams, params)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
return self.__execute_context(context)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File "/home/acbellorib/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)
ProgrammingError: (ProgrammingError) 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=?, tool_version=?, metadata=? WHERE history_dataset_association.id = ?' ['2012-05-07 03:35:33.977226', 'join (GNU coreutils) 8.13\nCopyright (C) 2011 Free Software Foundation, Inc.\nLicen\xc3\xa7a GPLv3+: GNU GPL vers\xc3\xa3o 3 ou posterior <http://gnu.org/licenses/gpl.html>.\nEste \xc3\xa9 um software livre: voc\xc3\xaa \xc3\xa9 livre para modific\xc3\xa1-lo ou redistribu\xc3\xad-lo.\nN\xc3\xa3o h\xc3\xa1 NENHUM', '~610,000 lines', u'GKJUVNG01A0005\t0\tGeneDB\t1511989\t255\t236M1I99M\t*\t0\t0\tCTTGAACTCTTCTGACGTTACCCTGTCCCCGGCACCGCCGACACGACCGCCTCCTGTTTCTCTGGCCGCTGCAGGCGTCAAGGTCGACGCTGAGTTGTCACTGCTCGCGACGACTCCACCGAGAACAAGCGAGCAGGAGAACGGCGCAGACACGCGGTCCTTGAGTGCTCTGTCGACACTGGTTGCAGCGATGGAAGGCGGTGA\nGTCGTCGACGCTGCTTCCACGGGCTCCTCCTGCCCCCGCGCACCAACACTGGTAAGCCCAGCGTGGCGTCAAGGCGGGCTGTAGCCTCGGCGGACAAGGGTGCCGTGAAAAGNGAGTCGCCAACGTCTTCCA\t*\n\nGKJUVNG01A0016\t0\tGeneDB\t71861\t255\t79M\t*\t0\t0\tTTCTGCATCCCGCTCCTGGGCACACATCGTGAGAGTAGCACCTGTGCACTCGCTCTCGCTGTCGCACCACGCTTCGCGT\t*\n\nGKJUVNG01A001C\t16\tGeneDB\t1482878\t255\t7H48M1D229M1I15M\t*\t0\t0\tATCAGCCGCCTCGAGGCACACGAGAGCGACGTCACCGAGCGCCTTGAGCACAGTACCAGCGAACGACAGCGCAGCTGACGTCGTTGGAGAAGGACATGCGCTTTCGCCTTCAGCAACTAGCCGACGCAGATCGCAAGGAGCGGGCGGCAGCGGCGGACCGGCAAACGGCCTTGCTCGAGTCCCTGGCCGCCCTCCG\nCGGCGAGCCGGCTGCCGTGTCTGCGGAGGGCATGACGGAGACGATGCTGCGACAGCTCATACATCTCATAGAGGCGGGGATGGGGGAAGGTACAGGC\t*\n\nGKJUVNG01A001K\t16\tGeneDB\t296529\t255\t286M3H\t*\t0\t0\tATTCCATCCAGTCGGCTCTTGCAGATTCTCAGTCGCGATCAGGAAGTGGTAGATCGCGCCCTTGGCGAGTCGGCTCAGCTCATCTTCCTGACAATTCTCCAGCTCTTCGGCATGGTGTGCTTCAACGCTATCCACTTCGGCCCTTTCATCGCTGTGCTTCCGATATCCGCGCTTCTCTTCTACCATCTGACGGTTCGCTTTCTATCC', '', <read-only buffer for 0x7f1958038e88, size -1, offset 0 at 0x7f19580565f0>, 516]