FASTQ Groomer tool

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FASTQ Groomer tool

fernandez Edgar

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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Re: FASTQ Groomer tool

fernandez Edgar

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 : '[hidden email]'
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/
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Re: FASTQ Groomer tool

Martin Čech
Hi Edgar,

it seems you are hitting this fail: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124 which hints that the tool is not properly loaded in the toolbox. Did you restart the server and handlers after you installed the tool? 
I cannot help with the MySQL as we do not usually test or run Galaxy on it. I understand that you did not update your Galaxy for 6 months?

Thank you for using Galaxy.

Martin

On Thu, Nov 5, 2015 at 2:20 PM Fernandez Edgar <[hidden email]> 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 : '[hidden email]'
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/

___________________________________________________________
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/
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Re: FASTQ Groomer tool

Nicola Soranzo-2
In reply to this post by fernandez Edgar
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 : '[hidden email]'
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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Re: FASTQ Groomer tool

fernandez Edgar

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:[hidden email]] De la part de Nicola Soranzo
Envoyé : November-05-15 2:33 PM
À : Fernandez Edgar; [hidden email]
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 : '[hidden email]'
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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: FASTQ Groomer tool

Martin Čech
Hi Edgar,

Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart.


Thank you for using Galaxy.

M.

On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar <[hidden email]> wrote:

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:[hidden email]] De la part de Nicola Soranzo
Envoyé : November-05-15 2:33 PM
À : Fernandez Edgar; [hidden email]
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 : '[hidden email]'
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/

 

___________________________________________________________
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:
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___________________________________________________________
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:
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R: Re: FASTQ Groomer tool

Nicola Soranzo-2
Hi Edgar,
to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart.

Cheers,
Nicola

---- Martin Čech ha scritto ----

Hi Edgar,

Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart.


Thank you for using Galaxy.

M.

On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar <[hidden email]> wrote:

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:[hidden email]] De la part de Nicola Soranzo
Envoyé : November-05-15 2:33 PM
À : Fernandez Edgar; [hidden email]
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 : '[hidden email]'
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/

 

___________________________________________________________
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/

___________________________________________________________
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:
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Re: R: Re: FASTQ Groomer tool

fernandez Edgar
Thank you so much guys!
I appreciate your help immensely!

On Nov 5, 2015 7:12 PM, Nicola Soranzo <[hidden email]> wrote:
Hi Edgar,
to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart.

Cheers,
Nicola

---- Martin Čech ha scritto ----

Hi Edgar,

Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart.

I updated the wiki (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to make it more clear.

Thank you for using Galaxy.

M.

On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar <[hidden email]<mailto:[hidden email]>> wrote:

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:[hidden email]<mailto:[hidden email]>] De la part de Nicola Soranzo
Envoyé : November-05-15 2:33 PM
À : Fernandez Edgar; [hidden email]<mailto:[hidden email]>
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 : '[hidden email]<mailto:[hidden email]>'
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<http://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<http://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<http://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<http://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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___________________________________________________________
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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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