Hello Nicola and Martin,

The service galaxy restart worked.
Can you guys give me a small explanation please?
Just for my understanding…

Cordialement / Regards,
Edgar Fernandez

De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola 
Soranzo
Envoyé : November-05-15 2:33 PM
À : Fernandez Edgar; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] FASTQ Groomer tool

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<mailto: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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