The issue here is the last line:

OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info("dataset")' ()

Do you have any security rules setup on the server, quotes, disk
issues, etc? You can always run a strace on run.sh for a better
understanding of whats going on.

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu

On Thu, Aug 8, 2013 at 4:12 AM, Jurgens de Bruin <debrui...@gmail.com> wrote:
> To all,
>
> I am getting the following error when I run sh run.sh :
>
> galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite>=2 egg
> successfully loaded for sqlite dialect
> Traceback (most recent call last):
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 35, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in
> __init__
>     create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options, app=self )
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 51, in create_or_verify_database
>     dataset_table = Table( "dataset", meta, autoload=True )
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 318, in __new__
>     table._init(name, metadata, *args, **kw)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 381, in _init
>     self._autoload(metadata, autoload_with, include_columns)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/schema.py",
> line 408, in _autoload
>     self, include_columns, exclude_columns
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 2425, in run_callable
>     return conn.run_callable(callable_, *args, **kwargs)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1968, in run_callable
>     return callable_(self, *args, **kwargs)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
> line 260, in reflecttable
>     return insp.reflecttable(table, include_columns, exclude_columns)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 370, in reflecttable
>     for col_d in self.get_columns(table_name, schema, **tblkw):
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 223, in get_columns
>     **kw)
>   File "<string>", line 1, in <lambda>
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/reflection.py",
> line 47, in cache
>     ret = fn(self, con, *args, **kw)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py",
> line 713, in get_columns
>     (pragma, qtable)))
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1449, in execute
>     params)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1628, in _execute_text
>     statement, parameters
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1698, in _execute_context
>     context)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1691, in _execute_context
>     context)
>   File
> "/scratch/sysusers/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
> line 331, in do_execute
>     cursor.execute(statement, parameters)
> OperationalError: (OperationalError) disk I/O error u'PRAGMA
> table_info("dataset")' ()
>
> Please any help would be appreciated!!
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to