Hi all,
I have fired up an cloud instance of Galaxy, 2 persistent nodes,
scalable up to 10. I have updated the code to the latest stable, after
issues with not being able to select multiple input for workflows
(more background:
http://dev.list.galaxyproject.org/selecting-multiple-inputs-for-workflows-not-possible-anymore-td4659827.html)
Running a workflow on multiple inputs (#=58) gives me - after a very
long page loading - this error:
************************************************
Internal Server Error
Galaxy was unable to sucessfully complete your request
URL:
http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910
Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>app_iter
*=* self*.*application*(*environ*,* sr_checker*)*|
Module paste.recursive:*84* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*633* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*128* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*handle_request*(* environ*,* start_response *)*|
Module galaxy.web.framework.base:*184* in |handle_request|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>body
*=* method*(* trans*,* ****kwargs *)*|
Module galaxy.webapps.galaxy.controllers.workflow:*1443* in |run|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*,*
out_data *=* tool*.*execute*(* trans*,* step*.*state*.*inputs*,*
history*=*target_history*)*|
Module galaxy.tools:*2342* in |execute|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
self*.*tool_action*.*execute*(* self*,* trans*,*
incoming*=*incoming*,* set_output_hid*=*set_output_hid*,*
history*=*history*,* ****kwargs *)*|
Module galaxy.tools.actions:*397* in |execute|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>job*.*add_input_dataset*(*
name*,* dataset *)*|
Module galaxy.model:*247* in |add_input_dataset|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*input_datasets*.*append*(*
JobToInputDatasetAssociation*(* name*,* dataset *)* *)*|
Module ?:*4* in |__init__|
Module sqlalchemy.orm.state:*82* in |initialize_instance|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*return*
manager*.*events*.*original_init*(****mixed*[**1**:**]**,* ****kwargs*)*|
Module galaxy.model:*450* in |__init__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*dataset
*=* dataset|
Module sqlalchemy.orm.attributes:*150* in |__set__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*impl*.*set*(*instance_state*(*instance*)**,*
instance_dict*(*instance*)**,* value*,* None*)*|
Module sqlalchemy.orm.attributes:*590* in |set|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
*=* self*.*fire_replace_event*(*state*,* dict_*,* value*,* old*,*
initiator*)*|
Module sqlalchemy.orm.attributes:*610* in |fire_replace_event|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>value
*=* ext*.*set*(*state*,* value*,* previous*,* initiator *or* self*)*|
Module sqlalchemy.orm.unitofwork:*69* in |set|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>sess*.*add*(*newvalue*)*|
Module sqlalchemy.orm.session:*1091* in |add|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_state*(*state*)*|
Module sqlalchemy.orm.session:*1100* in |_save_or_update_state|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_save_or_update_impl*(*state*)*|
Module sqlalchemy.orm.session:*1267* in |_save_or_update_impl|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_update_impl*(*state*)*|
Module sqlalchemy.orm.session:*1259* in |_update_impl|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>self*.*_attach*(*state*)*|
Module sqlalchemy.orm.session:*1286* in |_attach|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#>*(*mapperutil*.*state_str*(*state*)**,*
state*.*key*)*|
*InvalidRequestError: Can't attach instance <HistoryDatasetAssociation
at 0x8591c50>; another instance with key (<class
'galaxy.model.HistoryDatasetAssociation'>, (200,)) is already present
in this session.*
extra data
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#extra_data>
full traceback
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#full_traceback>
text version
<http://ec2-54-226-11-122.compute-1.amazonaws.com/workflow/run?id=e967e0737bb63910#text_version>
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
************************************************
After clicking history refresh, the workflow is actually in progress!
It completes EXCEPT for the last dataset, which stays gray. Clicking
on rerun on this last dataset, gives me the error:
************************************************
Internal Server Error
Galaxy was unable to sucessfully complete your request
URL:
http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe
Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>app_iter
*=* self*.*application*(*environ*,* sr_checker*)*|
Module paste.recursive:*84* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*633* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*128* in |__call__|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*return*
self*.*handle_request*(* environ*,* start_response *)*|
Module galaxy.web.framework.base:*184* in |handle_request|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>body
*=* method*(* trans*,* ****kwargs *)*|
Module galaxy.webapps.galaxy.controllers.tool_runner:*142* in |rerun|
|>>
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#>*raise*
Exception*(*"Failed to get job information for dataset hid %d" *%*
data*.*hid*)*|
*Exception: Failed to get job information for dataset hid 112*
extra data
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#extra_data>
full traceback
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#full_traceback>
text version
<http://ec2-54-226-11-122.compute-1.amazonaws.com/tool_runner/rerun?id=091bca94365ddfbe#text_version>
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
********************************************************
I have to manually rerun the last job with the corresponding workflow.
Thanks,
Joachim
