galaxy_workflow_execution_error

galaxy.tools.actions INFO 2016-08-17 12:00:33,411 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] (2.869 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,411 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] complete, ready to flush (8.121 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,421 Flushed transaction for job Job[id=104615,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] (9.415 ms)
galaxy.tools.execute DEBUG 2016-08-17 12:00:33,421 Tool [toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] created job [104615] (44.832 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,450 Handled output named output for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0 (8.624 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,453 Added output datasets to history (2.456 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,461 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] (2.803 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,461 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] complete, ready to flush (7.962 ms)
galaxy.tools.actions INFO 2016-08-17 12:00:33,471 Flushed transaction for job Job[id=104616,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] (9.618 ms)
galaxy.tools.execute DEBUG 2016-08-17 12:00:33,471 Tool [toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0] created job [104616] (45.648 ms)
galaxy.tools.execute DEBUG 2016-08-17 12:00:33,475 Executed 14 job(s) for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0 request: (723.250 ms)
galaxy.managers.collections DEBUG 2016-08-17 12:00:33,502 Created collection with 14 elements
galaxy.workflow.run DEBUG 2016-08-17 12:00:33,842 Workflow step 19355 of invocation None invoked (1098.664 ms)
galaxy.tools ERROR 2016-08-17 12:00:33,907 Exception caught while attempting tool execution:
Traceback (most recent call last):
  File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1142, in handle_single_execution
    job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id, mapping_over_collection=mapping_over_collection, execution_cache=execution_cache )
  File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1220, in execute
    return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )
  File "/galaxy/galaxy-app/lib/galaxy/tools/actions/__init__.py", line 439, in execute
    handle_output( name, output )
  File "/galaxy/galaxy-app/lib/galaxy/tools/actions/__init__.py", line 295, in handle_output
    wrapped_params.params,
  File "/galaxy/galaxy-app/lib/galaxy/tools/parameters/wrapped.py", line 33, in params
    self.wrap_values( self.tool.inputs, params, skip_missing_values=not self.tool.check_values )
  File "/galaxy/galaxy-app/lib/galaxy/tools/parameters/wrapped.py", line 65, in wrap_values
    name=input.name )
  File "/galaxy/galaxy-app/lib/galaxy/tools/wrappers.py", line 315, in __init__
    list.__init__( self, map( to_wrapper, datasets ) )
  File "/galaxy/galaxy-app/lib/galaxy/tools/wrappers.py", line 311, in to_wrapper
    dataset = element.dataset_instance
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'dataset_instance'
galaxy.tools.execute WARNING 2016-08-17 12:00:33,927 There was a failure executing a job for tool [toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.4galaxy2] - Error executing tool: 'HistoryDatasetAssociation' object has no attribute 'dataset_instance'
galaxy.tools.execute DEBUG 2016-08-17 12:00:33,927 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.4galaxy2 request: (76.079 ms)
galaxy.workflow.run ERROR 2016-08-17 12:00:33,930 Failed to schedule Workflow[id=2168,name=gducker: 2015-10 RNA-Seq], problem occurred on WorkflowStep[index=10,type=tool].
Traceback (most recent call last):
  File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 163, in invoke
    jobs = self._invoke_step( step )
  File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 233, in _invoke_step
    jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step )
  File "/galaxy/galaxy-app/lib/galaxy/workflow/modules.py", line 1090, in execute
    raise Exception(message)
Exception: Failed to create 1 out of 1 job(s) for workflow step.
galaxy.workflow.run ERROR 2016-08-17 12:00:33,946 Failed to execute scheduled workflow.
Traceback (most recent call last):
  File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 82, in __invoke
    outputs = invoker.invoke()
  File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 163, in invoke
    jobs = self._invoke_step( step )
  File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 233, in _invoke_step
    jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step )
  File "/galaxy/galaxy-app/lib/galaxy/workflow/modules.py", line 1090, in execute
    raise Exception(message)
Exception: Failed to create 1 out of 1 job(s) for workflow step.
128.112.117.99 - - [17/Aug/2016:12:00:19 -0400] "POST /workflow/run?id=c5edc4f5be0bec75 HTTP/1.1" 500 - "https://galaxy.princeton.edu/workflow/run?id=c5edc4f5be0bec75" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743
.116 Safari/537.36"
Error - <type 'exceptions.Exception'>: Failed to create 1 out of 1 job(s) for workflow step.
URL: https://galaxy.princeton.edu/workflow/run?id=c5edc4f5be0bec75
File '/galaxy/galaxy-app/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__
  app_iter = self.application(environ, sr_checker)
File '/galaxy/galaxy-app/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__
  return self.application(environ, start_response)
File '/galaxy/galaxy-app/lib/galaxy/web/framework/middleware/remoteuser.py', line 175 in __call__
  return self.app( environ, start_response )
File '/galaxy/galaxy-app/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__
  return self.application(environ, start_response)
File '/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line 131 in __call__
  return self.handle_request( environ, start_response )
File '/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File '/galaxy/galaxy-app/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1112 in run
  workflow_run_config=run_config
File '/galaxy/galaxy-app/lib/galaxy/workflow/run.py', line 22 in invoke
  return __invoke( trans, workflow, workflow_run_config, workflow_invocation, populate_state )
File '/galaxy/galaxy-app/lib/galaxy/workflow/run.py', line 82 in __invoke
  outputs = invoker.invoke()
File '/galaxy/galaxy-app/lib/galaxy/workflow/run.py', line 163 in invoke
  jobs = self._invoke_step( step )
File '/galaxy/galaxy-app/lib/galaxy/workflow/run.py', line 233 in _invoke_step
  jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step )
File '/galaxy/galaxy-app/lib/galaxy/workflow/modules.py', line 1090 in execute
  raise Exception(message)
Exception: Failed to create 1 out of 1 job(s) for workflow step.


CGI Variables
-------------
  CONTENT_LENGTH: '7765'
  CONTENT_TYPE: 'application/x-www-form-urlencoded'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate, br'
  HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.8'
  HTTP_CACHE_CONTROL: 'max-age=0'
  HTTP_CONNECTION: 'Keep-Alive'
  HTTP_COOKIE: '__unam=e8863f8-154bb6e7185-2da6898b-1; galaxysession=c77fb8aa0ff46ce0c320b2b51d094d3881ad7ab9d9b46ab27bcdbeac0ac0b12b20e6d54505bc01af; HTSEQ_BIODB_SID=53164; HTSEQ_BIODB_USERID=LPARSONS; MOD_AUTH_CAS_S=337cdcb1f4db7c923bdce27022e86c46'
    HTTP_DNT: '1'
  HTTP_HOST: 'galaxy.princeton.edu'
  HTTP_ORIGIN: 'https://galaxy.princeton.edu'
  HTTP_REFERER: 'https://galaxy.princeton.edu/workflow/run?id=c5edc4f5be0bec75'
  HTTP_REMOTE_USER: 'lparsons@princeton.edu'
  HTTP_UPGRADE_INSECURE_REQUESTS: '1'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '128.112.117.99'
  HTTP_X_FORWARDED_HOST: 'galaxy.princeton.edu'
  HTTP_X_FORWARDED_SERVER: 'galaxy.princeton.edu'
  HTTP_X_URL_SCHEME: 'https'
  ORGINAL_HTTP_HOST: 'localhost:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/workflow/run'
  QUERY_STRING: 'id=c5edc4f5be0bec75'
  REMOTE_ADDR: '128.112.117.99'
  REQUEST_METHOD: 'POST'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
    SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x7f4379317fd0>
  controller_action_key: u'web.workflow.run'
  is_api_request: False
  original_wsgi.url_scheme: 'http'
  paste.cookies: (<SimpleCookie: HTSEQ_BIODB_SID='53164' HTSEQ_BIODB_USERID='LPARSONS' MOD_AUTH_CAS_S='337cdcb1f4db7c923bdce27022e86c46' __unam='e8863f8-154bb6e7185-2da6898b-1' galaxysession='c77fb8aa0ff46ce0c320b2b51d094d3881ad7ab9d9b46ab27bcdbeac0ac0b12b20e6d54505bc01af
'>, '__unam=e8863f8-154bb6e7185-2da6898b-1; galaxysession=c77fb8aa0ff46ce0c320b2b51d094d3881ad7ab9d9b46ab27bcdbeac0ac0b12b20e6d54505bc01af; HTSEQ_BIODB_SID=53164; HTSEQ_BIODB_USERID=LPARSONS; MOD_AUTH_CAS_S=337cdcb1f4db7c923bdce27022e86c46')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f4379317a50>
  paste.httpserver.proxy.host: 'dummy'
  paste.httpserver.proxy.scheme: 'http'
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f437bf73590>
  paste.parsed_querystring: ([('id', 'c5edc4f5be0bec75')], 'id=c5edc4f5be0bec75')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'b25f95e6649311e6964b3cfdfe008f40'
  webob._body_file: (<_io.BufferedReader>, <socket._fileobject object at 0x7f437a9606d0 length=7765>)
  webob._parsed_post_vars: (MultiDict([('19346|tool_state', u'eyJpbnB1dCI6ICJudWxsIiwgIl9fcmVydW5fcmVtYXBfam9iX2lkX18iOiBudWxsLCAiX19wYWdlX18iOiAwfQ=='), ('19346|multi_mode', u'matched'), ('19346|input', u'1331'), ('19346|__force_update__input', u'true'), ('19347|tool_sta
te', u'eyJpbnB1dCI6ICJudWxsIiwgIl9fcmVydW5fcmVtYXBfam9iX2lkX18iOiBudWxsLCAiX19wYWdlX18iOiAwfQ=='), ('19347|multi_mode', u'matched'), ('19347|input', u'255031'), ('19347|__force_update__input', u'true'), ('19348|tool_state', u'eyJpbnB1dCI6ICJudWxsIiwgIl9fcmVydW5fcmVtYXBfam
9iX2lkX18iOiBudWxsLCAiX19wYWdlX18iOiAwfQ=='), ('19348|multi_mode', u'matched'), ('19348|input', u'255030'), ('19348|__force_update__input', u'true'), ('19349|tool_state', u'eyJjb3VudCI6ICJcIjFcIiIsICJlcnJvcl9yYXRlIjogIlwiMC4xXCIiLCAibWF0Y2hfcmVhZF93aWxkY2FyZHMiOiAiXCJmYWx
zZVwiIiwgInBhaXJlZF9lbmQiOiAie1wicGFpcmVkX2VuZF9ib29sZWFuXCI6IFwiZmFsc2VcIiwgXCJfX2N1cnJlbnRfY2FzZV9fXCI6IDF9IiwgIl9fcGFnZV9fIjogMCwgIm91dHB1dF9wYXJhbXMiOiAie1wib3V0cHV0X3R5cGVcIjogXCJkZWZhdW... 0x7f437c478170>)
  webob._parsed_query_vars: (GET([(u'id', u'c5edc4f5be0bec75')]), 'id=c5edc4f5be0bec75')
  webob.is_body_seekable: True
  wsgi process: 'Multithreaded'
------------------------------------------------------------