Hi will see what the problem with sqlite is and give feedback later....

On 8 August 2013 19:14, Nate Coraor <n...@bx.psu.edu> wrote:

> On Aug 8, 2013, at 12:50 PM, Adam Brenner wrote:
>
> > 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.
>
> Specifically, this appears to be a problem with the SQLite database file,
> galaxy-dist/database/universe.sqlite.
>
> --nate
>
> >
> > --
> > 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/
> >
>
>


-- 
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/

Reply via email to