Hi Edgar,
you can try to restart Galaxy (both web and handler processes) and re-run the tool.


Cheers,
Nicola

On 05/11/15 19:18, Fernandez Edgar wrote:

Hello again,

I installed today the tool : fastq_all_to_sanger

I get the same SQL error with that one too.

Any ideas guys?

Thank you!!!

Cordialement / Regards,

Edgar Fernandez

*De :*Fernandez Edgar
*Envoyé :* November-04-15 8:58 AM
*À :* 'galaxy-...@bx.psu.edu'
*Objet :* [galaxy-dev] FASTQ Groomer tool

Hello gents,

I just installed "FASTQ Groomer tool" for the teachers to try it out and I’ve been getting the following error than I do not understand:

galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756

galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' removed from tool config, unable to run job

galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756

Traceback (most recent call last):

File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in __monitor_step

    job_state = self.__check_job_state( job )

File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in __check_job_state

    state, job_destination = self.__verify_job_ready( job, job_wrapper )

File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready

    job_wrapper.fail( e )

File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail

    self.sa_session.flush()

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do

    return getattr(self.registry(), name)(*args, **kwargs)

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in flush

    self._flush(objects)

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in _flush

transaction.rollback(_capture_exception=True)

File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, in __exit__

compat.reraise(exc_type, exc_value, exc_tb)

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in _flush

    flush_context.execute()

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, in execute

    rec.execute(self)

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, in execute

    uow

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, in save_obj

    mapper, table, update)

File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, in _emit_update_statements

    execute(statement, multiparams)

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in execute

    return meth(self, multiparams, params)

File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection

    return connection._execute_clauseelement(self, multiparams, params)

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement

    compiled_sql, distilled_params

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in _execute_context

    context)

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in _handle_dbapi_exception

    exc_info

File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in raise_from_cause

reraise(type(exception), exception, tb=exc_tb)

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in _execute_context

    context)

File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, in do_execute

    cursor.execute(statement, parameters)

File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute

    self.errorhandler(self, exc, value)

File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler

    raise errorclass, errorvalue

ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE history_dataset_association.id = 1498' at line 1") [SQL: u'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id = %s'] [parameters: (datetime.datetime(2015, 11, 4, 13, 16, 20, 153739), ('This tool was disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 1498L)]

According to the tool shed repo, fastq_groomer is installed properly.

Mysql is at its latest for oracle linux 6:

[0]# mysql --version

mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1

[0]# rpm -qa | grep -i mysql

mysql-5.1.73-5.el6_6.x86_64

The only thing I have not done is update galaxy for the last 6 months because they’re students using it and I do not want to change anything while it’s in production.

I’m a little bit lost: Would you please indicate what I should check next?

Cordialement / Regards,

**

*Edgar Fernandez*

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

(Bur. : *1-514-343-6111 poste 16568**//*

*//*

*/Université de Montréal/**//*

PAVILLON ROGER-GAUDRY, bureau X-218



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