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!!
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/ 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
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/
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
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/
Hi will see what the problem with sqlite is and give feedback later....
On 8 August 2013 19:14, Nate Coraor nate@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/ 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
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/
galaxy-dev@lists.galaxyproject.org
-
Adam Brenner -
Jurgens de Bruin -
Nate Coraor