Hi Can,
something went wrong with your join utility part of your Ubuntu
installation.
Can you translate that for us?
'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'
If the data is not confidential and small enough, maybe you can send it
me. Also please make sure that no unicode character are included in the
dataset or description.
I do not think an reinstallation will solve that problem.
Cheers,
Bjoern
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
