Hi Xiaofei,

SQLite is not suitable for complex tasks like running workflows. Please
switch to PostgreSQL:


https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server

--nate

On Fri, Apr 4, 2014 at 1:35 PM, Wang, Xiaofei <xfw...@ku.edu> wrote:

>  Dear there,
>
>  I got this error when I run CloudMap EMS Variant Density Mapping
> workflow for Depth of Coverage on the local Galaxy instance on Mac. In
> fact, it works fine for Depth of Coverage when I run another workflow
> (Unmapped Mutant workflow) locally.
>
>  I really appreciate you guys for helping me to figure out so many
> problems! Thanks a lot!
>
>  Best,
>
>  Xiaofei
>
> Traceback (most recent call last):
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>  line 152, in prepare_job
>     job_wrapper.prepare()
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/__init__.py", line 
> 652, in prepare
>     if job.user is None and job.galaxy_session is None:
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py",
>  line 168, in __get__
>     return self.impl.get(instance_state(instance),dict_)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py",
>  line 453, in get
>     value = self.callable_(state, passive)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py",
>  line 508, in _load_for_state
>     return self._emit_lazyload(session, state, ident_key)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py",
>  line 552, in _emit_lazyload
>     return q._load_on_ident(ident_key)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
>  line 2512, in _load_on_ident
>     return q.one()
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
>  line 2184, in one
>     ret = list(self)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
>  line 2227, in __iter__
>     return self._execute_and_instances(context)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py",
>  line 2242, in _execute_and_instances
>     result = conn.execute(querycontext.statement, self._params)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
>  line 1449, in execute
>     params)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
>  line 1584, in _execute_clauseelement
>     compiled_sql, distilled_params
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
>  line 1698, in _execute_context
>     context)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py",
>  line 1691, in _execute_context
>     context)
>   File 
> "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/default.py",
>  line 331, in do_execute
>     cursor.execute(statement, parameters)
> OperationalError: (OperationalError) database is locked u'SELECT 
> galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS 
> galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, 
> galaxy_user.email AS galaxy_user_email, galaxy_user.username AS 
> galaxy_user_username, galaxy_user.password AS galaxy_user_password, 
> galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS 
> galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, 
> galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS 
> galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, 
> galaxy_user.activation_token AS galaxy_user_activation_token \nFROM 
> galaxy_user \nWHERE galaxy_user.id = ?' (1,)
>
>
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