Question: Issues with extracting galaxy workflow?
0
gravatar for mshortr
3.2 years ago by
mshortr0
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?

Thanks,
Megan

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.

URL: http://127.0.0.1:8080/workflow/build_from_current_history

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
1
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour