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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