Hello,
I am using the galaxy built-in database, SQLAlchemy on top of sql lite?
May I swith to postgress?
Regards
On 5 February 2015 at 14:41, Hans-Rudolf Hotz <[email protected]
<mailto:[email protected]>> wrote:
Hi Roberto
just double checking: are you using a PostgreSQL database, or are
you relying on the built in SQLite?
Hans-Rudolf
On 02/05/2015 02:26 PM, Roberto Alonso CIPF wrote:
Hello,
I am trying to use parallelism in Galaxy. I added this entry to the
tool xml config:
<tool id="fa_gc_content_1" name="Compute GC content">
<description>for each sequence in a file</description>
<parallelism method="basic" split_size="8"
split_mode="number_of_parts"><__/parallelism>
But when I run the job, the log shows the next:
Traceback (most recent call last):
File
"/home/ralonso/galaxy-dist/__lib/galaxy/jobs/runners/____init__.py",
line 158, in prepare_job
job_wrapper.prepare()
File
"/home/ralonso/galaxy-dist/__lib/galaxy/jobs/__init__.py", line
1607, in prepare
tool_evaluator.set_compute___environment(
compute_environment )
File
"/home/ralonso/galaxy-dist/__lib/galaxy/tools/evaluation.__py", line
53, in set_compute_environment
incoming = self.tool.params_from_strings( incoming, self.app )
File
"/home/ralonso/galaxy-dist/__lib/galaxy/tools/__init__.py", line
2810, in params_from_strings
return params_from_strings( self.inputs, params, app,
ignore_errors )
File
"/home/ralonso/galaxy-dist/__lib/galaxy/tools/parameters/____init__.py",
line 103, in params_from_strings
value = params[key].value_from_basic( value, app,
ignore_errors )
File
"/home/ralonso/galaxy-dist/__lib/galaxy/tools/parameters/__basic.py",
line
162, in value_from_basic
return self.to_python( value, app )
File
"/home/ralonso/galaxy-dist/__lib/galaxy/tools/parameters/__basic.py",
line
1999, in to_python
return app.model.context.query(
app.model.__HistoryDatasetAssociation
).get( int( value ) )
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/orm/query.py",
line 775, in get
return self._load_on_ident(key)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/orm/query.py",
line 2512, in _load_on_ident
return q.one()
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/orm/query.py",
line 2184, in one
ret = list(self)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/orm/query.py",
line 2227, in __iter__
return self._execute_and_instances(__context)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/orm/query.py",
line 2242, in _execute_and_instances
result = conn.execute(querycontext.__statement, self._params)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/home/ralonso/galaxy-dist/__eggs/SQLAlchemy-0.7.9-py2.7-__linux-x86_64-ucs4.egg/__sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) database is locked u'SELECT
history_dataset_association.id
<http://history_dataset_association.id>
<http://history_dataset___association.id
<http://history_dataset_association.id>>
AS history_dataset_association___id,
history_dataset_association.__history_id AS
history_dataset_association___history_id,
history_dataset_association.__dataset_id AS
history_dataset_association___dataset_id,
history_dataset_association.__create_time AS
history_dataset_association___create_time,
history_dataset_association.__update_time AS
history_dataset_association___update_time,
history_dataset_association.__state AS
history_dataset_association___state,
history_dataset_association.__copied_from_history_dataset___association_id
AS
history_dataset_association___copied_from_history_dataset___association_id,
history_dataset_association.__copied_from_library_dataset___dataset_association_id
AS
history_dataset_association___copied_from_library_dataset___dataset_association_id,
history_dataset_association.__hid AS
history_dataset_association___hid,
history_dataset_association.__name
<http://history_dataset_association.name>
<http://history_dataset___association.name
<http://history_dataset_association.name>> AS
history_dataset_association___name,
history_dataset_association.__info
<http://history_dataset_association.info>
<http://history_dataset___association.info
<http://history_dataset_association.info>> AS
history_dataset_association___info,
history_dataset_association.__blurb AS
history_dataset_association___blurb,
history_dataset_association.__peek AS
history_dataset_association___peek,
history_dataset_association.__tool_version AS
history_dataset_association___tool_version,
history_dataset_association.__extension AS
history_dataset_association___extension,
history_dataset_association.__metadata AS
history_dataset_association___metadata,
history_dataset_association.__parent_id AS
history_dataset_association___parent_id,
history_dataset_association.__designation AS
history_dataset_association___designation,
history_dataset_association.__deleted AS
history_dataset_association___deleted,
history_dataset_association.__purged
AS history_dataset_association___purged,
history_dataset_association.__visible AS
history_dataset_association___visible,
history_dataset_association.__hidden_beneath_collection___instance_id
AS
history_dataset_association___hidden_beneath_collection___instance_id,
history_dataset_association.__extended_metadata_id AS
history_dataset_association___extended_metadata_id, dataset_1.id
<http://dataset_1.id>
<http://dataset_1.id> AS dataset_1_id, dataset_1.create_time AS
dataset_1_create_time, dataset_1.update_time AS
dataset_1_update_time,
dataset_1.state AS dataset_1_state, dataset_1.deleted AS
dataset_1_deleted, dataset_1.purged AS dataset_1_purged,
dataset_1.purgable AS dataset_1_purgable,
dataset_1.object_store_id AS
dataset_1_object_store_id, dataset_1.external_filename AS
dataset_1_external_filename, dataset_1._extra_files_path AS
dataset_1__extra_files_path, dataset_1.file_size AS
dataset_1_file_size,
dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS
dataset_1_uuid \nFROM history_dataset_association LEFT OUTER JOIN
dataset AS dataset_1 ON dataset_1.id <http://dataset_1.id>
<http://dataset_1.id> =
history_dataset_association.__dataset_id \nWHERE
history_dataset_association.id
<http://history_dataset_association.id>
<http://history_dataset___association.id
<http://history_dataset_association.id>> =
?' (1,)
galaxy.jobs.runners ERROR 2015-02-05 12:58:11,431 (89_486) Failure
preparing job
So when one task tries to run it fails, it seems that the
database is
locked by other task. When I run with 4 splits it never happen,
but with
5 it begins to happen. Indeed with 5 splits sometimes it doesn't
happen,
but since 6 it always occurs.
Could you please help me?
Regards
--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021 <tel:%2B34%20963289680%20Ext.%201021>
Fax: +34 963289574 <tel:%2B34%20963289574>
E-Mail: [email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
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--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: [email protected] <mailto:[email protected]>
