error in workflow

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error in workflow

Milad Bastami
Dear Galaxy Developers,
I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately).  Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size).
I will appreciate your help
Traceback (most recent call last):
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish
    self.sa_session.flush()
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush
    self._flush(objects)
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush
    transaction.commit()
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit
    t[1].commit()
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit
    self._do_commit()
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit
    self.connection._commit_impl()
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl
    self._handle_dbapi_exception(e, None, None, None, None)
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl
    self.engine.dialect.do_commit(self.connection)
  File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit
    connection.commit()
OperationalError: (OperationalError) database is locked None None

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Re: error in workflow

Hans-Rudolf Hotz
Hi Milad

The error message: "database is locked" might be a hint.

Are you using a PostgreSQL database or just SQLite ? If the latter, you
will often run in troubles when running more than one job at a time, due
to file locking.

Regards, Hans-Rudolf


On 03/11/2014 07:41 PM, Milad Bastami wrote:

> Dear Galaxy Developers,
> I'm running galaxy local on ubuntu and trying to run a workflow on
> multiple datasets (separately).  Occasionally when I try to run workflow
> on input dataset I get "Unable to finish job" error in some steps, in
> most time the problem will be solved when I run the workflow again, but
> this going to happen more frequently. I attached the error message here.
> I suspect it may be related to increase in number of datasets of the
> current history (1757 datasets with ~350GB size).
> I will appreciate your help
>
> Traceback (most recent call last):
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job
>      job_wrapper.finish( stdout, stderr, exit_code )
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish
>      self.sa_session.flush()
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do
>      return getattr(self.registry(), name)(*args, **kwargs)
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush
>      self._flush(objects)
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush
>      transaction.commit()
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit
>      t[1].commit()
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit
>      self._do_commit()
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit
>      self.connection._commit_impl()
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl
>      self._handle_dbapi_exception(e, None, None, None, None)
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl
>      self.engine.dialect.do_commit(self.connection)
>    File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit
>      connection.commit()
> OperationalError: (OperationalError) database is locked None None
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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can I change to PostgreSQL?

Milad Bastami
Many thanks for your help. Your are right about database (I'm using SQLite). I've found a tutorial at GMOD (http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work with PostgreSQL, but can I change the current database to PostgreSQL without missing my datasets? I am running a single-user galaxy instance.

Cheers, Milad


> Date: Wed, 12 Mar 2014 09:07:00 +0100

> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
> Subject: Re: [galaxy-dev] error in workflow
>
> Hi Milad
>
> The error message: "database is locked" might be a hint.
>
> Are you using a PostgreSQL database or just SQLite ? If the latter, you
> will often run in troubles when running more than one job at a time, due
> to file locking.
>
> Regards, Hans-Rudolf
>
>
> On 03/11/2014 07:41 PM, Milad Bastami wrote:
> > Dear Galaxy Developers,
> > I'm running galaxy local on ubuntu and trying to run a workflow on
> > multiple datasets (separately). Occasionally when I try to run workflow
> > on input dataset I get "Unable to finish job" error in some steps, in
> > most time the problem will be solved when I run the workflow again, but
> > this going to happen more frequently. I attached the error message here.
> > I suspect it may be related to increase in number of datasets of the
> > current history (1757 datasets with ~350GB size).
> > I will appreciate your help
> >
> > Traceback (most recent call last):
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job
> > job_wrapper.finish( stdout, stderr, exit_code )
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish
> > self.sa_session.flush()
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do
> > return getattr(self.registry(), name)(*args, **kwargs)
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush
> > self._flush(objects)
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush
> > transaction.commit()
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit
> > t[1].commit()
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit
> > self._do_commit()
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit
> > self.connection._commit_impl()
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl
> > self._handle_dbapi_exception(e, None, None, None, None)
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl
> > self.engine.dialect.do_commit(self.connection)
> > File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit
> > connection.commit()
> > OperationalError: (OperationalError) database is locked None None
> >
> >
> >
> > ___________________________________________________________
> > 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:
> > http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/mailinglists/
> >

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: can I change to PostgreSQL?

Hans-Rudolf Hotz

Have a look at
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server

on how to set up the PostgreSQL database for Galaxy.

I am not aware of any tools to port the contents of the SQLite file to a
PostgreSQL database, except for setting up an all new Galaxy server
(running with PostgreSQL) and exporting the important histories from
your old server followed by importing them into your new server - though
looking at the size of your history, this might not work.


Hans-Rudolf

On 03/12/2014 09:57 AM, Milad Bastami wrote:

> Many thanks for your help. Your are right about database (I'm using
> SQLite). I've found a tutorial at GMOD
> (http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work
> with PostgreSQL, but can I change the current database to PostgreSQL
> without missing my datasets? I am running a single-user galaxy instance.
>
> Cheers, Milad
>
>
>  > Date: Wed, 12 Mar 2014 09:07:00 +0100
>  > From: [hidden email]
>  > To: [hidden email]
>  > CC: [hidden email]
>  > Subject: Re: [galaxy-dev] error in workflow
>  >
>  > Hi Milad
>  >
>  > The error message: "database is locked" might be a hint.
>  >
>  > Are you using a PostgreSQL database or just SQLite ? If the latter, you
>  > will often run in troubles when running more than one job at a time, due
>  > to file locking.
>  >
>  > Regards, Hans-Rudolf
>  >PostgreSQL
>  >
>  > On 03/11/2014 07:41 PM, Milad Bastami wrote:
>  > > Dear Galaxy Developers,
>  > > I'm running galaxy local on ubuntu and trying to run a workflow on
>  > > multiple datasets (separately). Occasionally when I try to run workflow
>  > > on input dataset I get "Unable to finish job" error in some steps, in
>  > > most time the problem will be solved when I run the workflow again, but
>  > > this going to happen more frequently. I attached the error message
> here.
>  > > I suspect it may be related to increase in number of datasets of the
>  > > current history (1757 datasets with ~350GB size).
>  > > I will appreciate your help
>  > >
>  > > Traceback (most recent call last):
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py",
> line 116, in queue_job
>  > > job_wrapper.finish( stdout, stderr, exit_code )
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py",
> line 1068, in finish
>  > > self.sa_session.flush()
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
> line 114, in do
>  > > return getattr(self.registry(), name)(*args, **kwargs)
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
> line 1718, in flush
>  > > self._flush(objects)
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
> line 1804, in _flush
>  > > transaction.commit()
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
> line 365, in commit
>  > > t[1].commit()
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 2045, in commit
>  > > self._do_commit()
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 2075, in _do_commit
>  > > self.connection._commit_impl()
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1280, in _commit_impl
>  > > self._handle_dbapi_exception(e, None, None, None, None)
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
> line 1277, in _commit_impl
>  > > self.engine.dialect.do_commit(self.connection)
>  > > File
> "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
> line 307, in do_commit
>  > > connection.commit()
>  > > OperationalError: (OperationalError) database is locked None None
>  > >
>  > >
>  > >
>  > > ___________________________________________________________
>  > > 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:
>  > > http://lists.bx.psu.edu/
>  > >
>  > > 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:
  http://lists.bx.psu.edu/

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