Question: Issues with extracting galaxy workflow?
gravatar for mshortr
3.2 years ago by
United States
mshortr0 wrote:

Hi all,

Has anyone had issues with extracting Galaxy workflows from a history before? I will add more information later (a screenshot of the error I am getting) but for now, it looks like it may be timing out before it extracts the workflow. Keep in mind, I am running Galaxy on a VirtualMachine on my Windows PC so perhaps power might be a problem. Is it possible for a workflow to timeout? I tried it on a smaller subset of the history (about 1/4 to 1/2 of the full workflow) and it was successful at creating a workflow.


Any ideas?


error workflow galaxy • 776 views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by mshortr0

Here is the error message: I am completely stumped. Has anyone run into this before?


Error Traceback:

View as:   Interactive  |  Text  |  XML (full)

Exception: Failed to extract job.


Module weberror.evalexception.middleware:364 in respond         view
>>  app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__         view
>>  return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__         view
>>  return self.application(environ, start_response)

Module galaxy.web.framework.base:133 in __call__         view
>>  return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:191 in handle_request         view
>>  body = method( trans, **kwargs )

Module galaxy.webapps.galaxy.controllers.workflow:1021 in build_from_current_history         view
>>  workflow_name=workflow_name

Module galaxy.workflow.extract:31 in extract_workflow         view
>>  steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids )

Module galaxy.workflow.extract:146 in extract_steps         view
>>  raise Exception( "Failed to extract job." )

Exception: Failed to extract job.

ADD REPLYlink written 3.2 years ago by shortridge.150
gravatar for Dannon Baker
3.2 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Can you check the Galaxy log?  It should have a line specifying which job extraction caused the failure.  From there, we can debug and might be able to fix the error.

ADD COMMENTlink written 3.2 years ago by Dannon Baker3.7k
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