One small problem for experts, one giant question for me..
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.
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 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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Dear Bjoern, I was using ubuntu with Turkish language. Your answer gave me clue about the problem. Turkish language contains some special characters that may confuse Galaxy. So, I turned it into English. Voila! Problem solved. :) Thank you so much Bjoern. :) You are the best! Can Holyavkin
participants (2)
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Bjoern Gruening -
Can Holyavkin