Depth of Coverage (local galaxy __ CloudMap)

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Depth of Coverage (local galaxy __ CloudMap)

Wang, Xiaofei
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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Re: Depth of Coverage (local galaxy __ CloudMap)

Nate Coraor (nate@bx.psu.edu)
Hi Xiaofei,

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


--nate

On Fri, Apr 4, 2014 at 1:35 PM, Wang, Xiaofei <[hidden email]> 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,)

___________________________________________________________
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/