Hello everyone,
Firstly, I am beginner. I am a new Galaxy user that installed the Galaxy
locally into my ubuntu (13.04) installed computer. Everything is working
perfectly right now. Galaxy is really awesome.
To learn the basics, I started the basic tutorial (Galaxy101
https://main.g2.bx.psu.edu/u/aun1/p/galaxy101) that helps too much. This
tutorial consist a step for explaning "Compare Two Datasets" function. I did
exactly everthing the instructor said however that module become red in History
with following error:
tool error
An error occured with dataset:
Unable to finish job (screenshot of error: http://i.imgur.com/xHqhK72.png)
I wrote the bug report at end of the mail.
Interestingly, when I press "View" button, I get the data that I wanted.
However, any metadata is seen. So I can not see the final results on the UCSC
browser. I replicate the same module at public server, it didn't gave an error.
What might cause this kind of problem? Does reinstalling solve this problem?
Would you please help me?
Thank you everyone.
Traceback (most recent call last):
File "/home/can/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 94, in
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/can/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009, in finish
self.sa_session.flush()
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1718, in flush
self._flush(objects)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1789, in _flush
flush_context.execute()
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 331, in execute
rec.execute(self)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 475, in execute
uow
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 59, in save_obj
mapper, table, update)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 485, in _emit_update_statements
execute(statement, params)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
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 job SET update_time=?, stdout=?, stderr=? WHERE
job.id = ?' ('2013-08-09 09:00:48.464260', 'join (GNU coreutils)
8.20\nCopyright (C) 2012 Free Software Foundation, Inc.\nLisans GPLv3+: GNU GPL
s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1 <http://gnu.org/licenses/gpl.html>.\nBu
\xc3\x96zg\xc3\xbcr bir yaz\xc4\xb1l\xc4\xb1md\xc4\xb1r:
de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f\xc4\xb1tmakta
\xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4\xb1n izin verdi\xc4\x9fi
\xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir GARANT\xc4\xb0 sunulmaz.\n\nMike
Haertel taraf\xc4\xb1ndan yaz\xc4\xb1ld\xc4\xb1.\n', '', 41)
Can Holyavkin
PhD Student
Istanbul Technical University
Molecular Biology and Genetics Dept.___________________________________________________________
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