Hi I can't promise, this is the solution for your specific problem, but you will always run into "database is locked" issue, when using SQLite. Hence, I strongly recommend to switch to a PostgreSQL database as the back-end for Galaxy (see also: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Swi... ) Hans-Rudolf On 02/05/2015 02:44 PM, Roberto Alonso CIPF wrote:
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 <hrh@fmi.ch <mailto:hrh@fmi.ch>> 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: ralonso@cipf.es <mailto:ralonso@cipf.es> <mailto:ralonso@cipf.es <mailto:ralonso@cipf.es>>
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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: ralonso@cipf.es <mailto:ralonso@cipf.es>