[galaxy-dev] Error executing workflow via API
Hi,
I execute a number of workflows via the API which all work fine. However,
the longest one I use (consists of three linked tasks), returns an error. I
call the workflow in the python script using popen and has the format:
/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py
d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/workflows
f597429621d6eb2b hist_id=f597429621d6eb2b 4=hda=c8c00aa41dc69085
The task appears on the history panel and all tasks eventually complete in the
workflow, however, the task that calls the workflow using the above popen call
returns the following error:
Traceback (most recent call last):
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line 31,
in module
main()
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line 28,
in main
submit( sys.argv[1], sys.argv[2], data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 117, in submit
r = post( api_key, url, data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 51, in post
return json.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/socket.py, line 351, in read
data = self._sock.recv(rbufsize)
File /usr/lib/python2.7/httplib.py, line 541, in read
return self._read_chunked(amt)
File /usr/lib/python2.7/httplib.py, line 586, in _read_chunked
raise IncompleteRead(''.join(value))
httplib.IncompleteRead: IncompleteRead(147 bytes read)
This worked on older versions of Galaxy. I need this to work so I can monitor
the workflow so know when all tasks are complete.
has anyone seen this error? Or got an idea how to solve it.
hg summary reports:
% hg summary
parent: 13771:7a4d321c0e38 tip
Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae
branch: stable
commit: (clean)
update: (current)
Thanks
Neil
___
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Re: [galaxy-dev] Error executing workflow via API
There are definitely limitations to the size of workflows that can be
executed right now but I feel like that problem should be getting
better not worse so this is a little confusing. Did something besides
the Galaxy version change (like proxy settings, timeouts, etc...?).
The client side error interesting but I feel like a server side error
would reveal more - is there a server side error in the Galaxy logs
for this?
-John
On Mon, Sep 8, 2014 at 9:29 PM, neil.burd...@csiro.au wrote:
Hi,
I execute a number of workflows via the API which all work fine.
However, the longest one I use (consists of three linked tasks), returns an
error. I call the workflow in the python script using popen and has the
format:
/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py
d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/workflows
f597429621d6eb2b hist_id=f597429621d6eb2b 4=hda=c8c00aa41dc69085
The task appears on the history panel and all tasks eventually complete in
the workflow, however, the task that calls the workflow using the above
popen call returns the following error:
Traceback (most recent call last):
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
31, in module
main()
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
28, in main
submit( sys.argv[1], sys.argv[2], data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 117, in
submit
r = post( api_key, url, data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 51, in post
return json.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/socket.py, line 351, in read
data = self._sock.recv(rbufsize)
File /usr/lib/python2.7/httplib.py, line 541, in read
return self._read_chunked(amt)
File /usr/lib/python2.7/httplib.py, line 586, in _read_chunked
raise IncompleteRead(''.join(value))
httplib.IncompleteRead: IncompleteRead(147 bytes read)
This worked on older versions of Galaxy. I need this to work so I can
monitor the workflow so know when all tasks are complete.
has anyone seen this error? Or got an idea how to solve it.
hg summary reports:
% hg summary
parent: 13771:7a4d321c0e38 tip
Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae
branch: stable
commit: (clean)
update: (current)
Thanks
Neil
___
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
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Error executing workflow via API
Hi John,
Thanks for the quick response. There seems to be nothing obvious on
the server side log. This is all I get:
galaxy.jobs.runners DEBUG 2014-09-09 11:43:23,850 (322) command is: python
/home/galaxy/milxcloud-new/tools/cte/cte_process_input_data.py
'/home/galaxy/milxcloud-new/tools/cte/cte_process_input_data.py'
'/home/galaxy/milxcloud-new/database/files/000/dataset_447.dat' 'Input data
(141-S-0851-MRI-T1-Screening)'
'/home/galaxy/milxcloud-new/database/files/000/dataset_447_files'
d2fcd3feb4c6318c496d55fa8869b67c
'/home/galaxy/milxcloud-new/database/files/000/dataset_454.dat'
'/home/galaxy/milxcloud-new/database/job_working_directory/000/322/dataset_454_files'
galaxy.jobs.runners.local DEBUG 2014-09-09 11:43:23,852 (322) executing job
script:
/home/galaxy/milxcloud-new/database/job_working_directory/000/322/galaxy_322.sh
galaxy.jobs DEBUG 2014-09-09 11:43:23,882 (322) Persisting job destination
(destination id: local:///)
127.0.0.1 - - [09/Sep/2014:11:43:23 +1000] POST
/new/api/workflows?key=d2fcd3feb4c6318c496d55fa8869b67c HTTP/1.1 200 - -
Python-urllib/2.7
I still have an 'old' version of Galaxy and so can confirm that this workflow
works fine on older versions of Galaxy.
With this 'latest' version of Galaxy I am using the default values stated in
universe_wsgi.ini . I am happy to modify values to see if I can resolve this
issue if you can suggest where /what I modify.
Also, in older versions of Galaxy after executing the popen command I get a
response almost immediately (and I do with other workflows I use). However, in
this particular case I don't get a response for 5 minutes.
Thanks
Neil
From: John Chilton [jmchil...@gmail.com]
Sent: Tuesday, September 09, 2014 11:37 AM
To: Burdett, Neil (DPS, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error executing workflow via API
There are definitely limitations to the size of workflows that can be
executed right now but I feel like that problem should be getting
better not worse so this is a little confusing. Did something besides
the Galaxy version change (like proxy settings, timeouts, etc...?).
The client side error interesting but I feel like a server side error
would reveal more - is there a server side error in the Galaxy logs
for this?
-John
On Mon, Sep 8, 2014 at 9:29 PM, neil.burd...@csiro.au wrote:
Hi,
I execute a number of workflows via the API which all work fine.
However, the longest one I use (consists of three linked tasks), returns an
error. I call the workflow in the python script using popen and has the
format:
/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py
d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/workflows
f597429621d6eb2b hist_id=f597429621d6eb2b 4=hda=c8c00aa41dc69085
The task appears on the history panel and all tasks eventually complete in
the workflow, however, the task that calls the workflow using the above
popen call returns the following error:
Traceback (most recent call last):
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
31, in module
main()
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
28, in main
submit( sys.argv[1], sys.argv[2], data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 117, in
submit
r = post( api_key, url, data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 51, in post
return json.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/socket.py, line 351, in read
data = self._sock.recv(rbufsize)
File /usr/lib/python2.7/httplib.py, line 541, in read
return self._read_chunked(amt)
File /usr/lib/python2.7/httplib.py, line 586, in _read_chunked
raise IncompleteRead(''.join(value))
httplib.IncompleteRead: IncompleteRead(147 bytes read)
This worked on older versions of Galaxy. I need this to work so I can
monitor the workflow so know when all tasks are complete.
has anyone seen this error? Or got an idea how to solve it.
hg summary reports:
% hg summary
parent: 13771:7a4d321c0e38 tip
Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae
branch: stable
commit: (clean)
update: (current)
Thanks
Neil
___
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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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org
Re: [galaxy-dev] Error executing workflow via API
Hi,
It seems all my other workflows that work have a txt output feeding into a
an input accepting a text input. This particular workflow (that's failing) is
outputting a html output to a html input ? Could this be the reason for the
failure? has anyone else got html outputs to inputs on their workflows ? Or
maybe on the wrong track again? The workflows are the same on this version of
Galaxy as they are on the older version that works.
Everything else remains the same i.e. same desktop etc...
Neil
From: Burdett, Neil (DPS, Herston - RBWH)
Sent: Tuesday, September 09, 2014 11:55 AM
To: John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Error executing workflow via API
Hi John,
Thanks for the quick response. There seems to be nothing obvious on
the server side log. This is all I get:
galaxy.jobs.runners DEBUG 2014-09-09 11:43:23,850 (322) command is: python
/home/galaxy/milxcloud-new/tools/cte/cte_process_input_data.py
'/home/galaxy/milxcloud-new/tools/cte/cte_process_input_data.py'
'/home/galaxy/milxcloud-new/database/files/000/dataset_447.dat' 'Input data
(141-S-0851-MRI-T1-Screening)'
'/home/galaxy/milxcloud-new/database/files/000/dataset_447_files'
d2fcd3feb4c6318c496d55fa8869b67c
'/home/galaxy/milxcloud-new/database/files/000/dataset_454.dat'
'/home/galaxy/milxcloud-new/database/job_working_directory/000/322/dataset_454_files'
galaxy.jobs.runners.local DEBUG 2014-09-09 11:43:23,852 (322) executing job
script:
/home/galaxy/milxcloud-new/database/job_working_directory/000/322/galaxy_322.sh
galaxy.jobs DEBUG 2014-09-09 11:43:23,882 (322) Persisting job destination
(destination id: local:///)
127.0.0.1 - - [09/Sep/2014:11:43:23 +1000] POST
/new/api/workflows?key=d2fcd3feb4c6318c496d55fa8869b67c HTTP/1.1 200 - -
Python-urllib/2.7
I still have an 'old' version of Galaxy and so can confirm that this workflow
works fine on older versions of Galaxy.
With this 'latest' version of Galaxy I am using the default values stated in
universe_wsgi.ini . I am happy to modify values to see if I can resolve this
issue if you can suggest where /what I modify.
Also, in older versions of Galaxy after executing the popen command I get a
response almost immediately (and I do with other workflows I use). However, in
this particular case I don't get a response for 5 minutes.
Thanks
Neil
From: John Chilton [jmchil...@gmail.com]
Sent: Tuesday, September 09, 2014 11:37 AM
To: Burdett, Neil (DPS, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Error executing workflow via API
There are definitely limitations to the size of workflows that can be
executed right now but I feel like that problem should be getting
better not worse so this is a little confusing. Did something besides
the Galaxy version change (like proxy settings, timeouts, etc...?).
The client side error interesting but I feel like a server side error
would reveal more - is there a server side error in the Galaxy logs
for this?
-John
On Mon, Sep 8, 2014 at 9:29 PM, neil.burd...@csiro.au wrote:
Hi,
I execute a number of workflows via the API which all work fine.
However, the longest one I use (consists of three linked tasks), returns an
error. I call the workflow in the python script using popen and has the
format:
/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py
d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/workflows
f597429621d6eb2b hist_id=f597429621d6eb2b 4=hda=c8c00aa41dc69085
The task appears on the history panel and all tasks eventually complete in
the workflow, however, the task that calls the workflow using the above
popen call returns the following error:
Traceback (most recent call last):
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
31, in module
main()
File /home/galaxy/milxcloud-new/scripts/api/workflow_execute.py, line
28, in main
submit( sys.argv[1], sys.argv[2], data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 117, in
submit
r = post( api_key, url, data )
File /home/galaxy/milxcloud-new/scripts/api/common.py, line 51, in post
return json.loads( urllib2.urlopen( req ).read() )
File /usr/lib/python2.7/socket.py, line 351, in read
data = self._sock.recv(rbufsize)
File /usr/lib/python2.7/httplib.py, line 541, in read
return self._read_chunked(amt)
File /usr/lib/python2.7/httplib.py, line 586, in _read_chunked
raise IncompleteRead(''.join(value))
httplib.IncompleteRead: IncompleteRead(147 bytes read)
This worked on older versions of Galaxy. I need this to work so I can
monitor the workflow so know when all tasks are complete.
has anyone seen this error? Or got an idea how to solve it.
hg summary reports:
% hg summary
parent: 13771:7a4d321c0e38 tip
Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae
branch: stable
commit
[galaxy-dev] Error running workflow via API
The API interface is translating my parameters into python repr strings instead of actual strings. A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NN NN /slipstream/galaxy/production/data/files/020/dataset_20664.dat is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NN /slipstream/galaxy/production/data/files/020/dataset_20728.dat The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10 First barcode NN Second (optional) barcode NN I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet. Thanks -john smime.p7s Description: S/MIME cryptographic signature ___ 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/
Re: [galaxy-dev] Error running workflow via API
I’ve figured this one out. The tool id changed one me. Sorry for the spam. -j On Apr 9, 2014, at 4:48 PM, John Marmaduke Eppley jmepp...@mit.edu wrote: The API interface is translating my parameters into python repr strings instead of actual strings. A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NN NN /slipstream/galaxy/production/data/files/020/dataset_20664.dat is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NN /slipstream/galaxy/production/data/files/020/dataset_20728.dat The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10 First barcode NN Second (optional) barcode NN I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet. Thanks -john ___ 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/ smime.p7s Description: S/MIME cryptographic signature ___ 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/
[galaxy-dev] Error running workflow via API
The API interface is translating my parameters into python repr strings instead of actual strings. A command that should look like this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta NN NN /slipstream/galaxy/production/data/files/020/dataset_20664.dat is getting run as this: createPrimerFile.py /minilims/galaxy-data/primerTemplates/nextera.2x.primers.fasta __lt__galaxy.tools.parameters.basic.RuntimeValue object at 0x792be10__gt__ NN /slipstream/galaxy/production/data/files/020/dataset_20728.dat The input table in the tool info page is: Input Parameter Value Note for rerun chemistry type: galaxy.tools.parameters.basic.RuntimeValue object at 0x7fee4425ca10 First barcode NN Second (optional) barcode NN I’m running a slightly out of date version of Galaxy (I think it is change set 11080:87b586afb054) because this is BioTeam’s Slipstream appliance. Is there any chance this is a known bug? I didn’t see anything in Trello, but I’m really not sure I’ve got the hang of Trello yet. Thanks -john___ 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/
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/ ___ 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/
[galaxy-dev] error in workflow
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 helpTraceback (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/
[galaxy-dev] error running workflow
Hi all, I have added some tools to my local install of Galaxy. To get to my final results I have to do a lot of steps. When I try to run every step separately it turns out to work out fine. But when I try to run all steps at once with a workflow I get the following error message. OperationalError: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02 11:34:48.135419', 'queued', 529] I have noticed that the processes eat a lot of my computer resources. Other than that I have no clue what the problem could be. Any tips are appreciated. Kind regards, Jaap van der Heijden ___ 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/
Re: [galaxy-dev] error running workflow
Hi Jaap are you using 'SQLite', if so, I recommend to switch to 'PostgreSQL', see: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server/#Switching_to_a_database_server Regards, Hans On 07/02/2012 02:26 PM, j.w.f.van_der_heij...@lumc.nl wrote: Hi all, I have added some tools to my local install of Galaxy. To get to my final results I have to do a lot of steps. When I try to run every step separately it turns out to work out fine. But when I try to run all steps at once with a workflow I get the following error message. |OperationalError: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02 11:34:48.135419', 'queued', 529] I have noticed that the processes eat a lot of my computer resources. Other than that I have no clue what the problem could be. Any tips are appreciated. Kind regards, Jaap van der Heijden | ___ 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/ ___ 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/
