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/
> aebrenne@uci.edu
>
> On Thu, Aug 8, 2013 at 4:12 AM, Jurgens de Bruin <debruinjj@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
>>
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