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
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/