Arvados

sguthrie@shell:~/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow$ arvados-cwl-runner --enable-reuse --local --project-uuid=su92l-j7d0g-6kmqy2uvstl8f93 main-hu34D5B9.cwl main-hu34D5B9-samples.json 
/home/sguthrie/new/bin/arvados-cwl-runner 1.0.20160519200217, arvados-python-client 0.1.20160517202250, cwltool 1.0.20160519182434
2016-05-23 18:46:36 arvados.cwl-runner[27364] INFO: Pipeline instance su92l-d1hrv-37c3rlf49pdp3vf
2016-05-23 18:46:37 arvados.cwl-runner[27364] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: <class 'cwltool.errors.WorkflowException'>
Workflow error, try again with --debug for more information:
  Workflow did not return a result.

arvados-cwl-runner --enable-reuse --local --project-uuid=su92l-j7d0g-6kmqy2uvstl8f93 main-hu34D5B9.cwl main-hu34D5B9-samples.json 
/home/sguthrie/new/bin/arvados-cwl-runner 1.0.20160519200217, arvados-python-client 0.1.20160517202250, cwltool 1.0.20160519182434
2016-05-23 18:46:36 arvados.cwl-runner[27364] INFO: Pipeline instance su92l-d1hrv-37c3rlf49pdp3vf
2016-05-23 18:46:37 arvados.cwl-runner[27364] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: <class 'cwltool.errors.WorkflowException'>
Workflow error, try again with --debug for more information:
  Workflow did not return a result.
(new)sguthrie@shell:~/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow$ arvados-cwl-runner --enable-reuse --local --debug --project-uuid=su92l-j7d0g-6kmqy2uvstl8f93 main-hu34D5B9.cwl main-hu34D5B9-samples.json 
/home/sguthrie/new/local/lib/python2.7/site-packages/pkg_resources.py:991: UserWarning: /home/sguthrie/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
  warnings.warn(msg, UserWarning)
/home/sguthrie/new/bin/arvados-cwl-runner 1.0.20160519200217, arvados-python-client 0.1.20160517202250, cwltool 1.0.20160519182434
2016-05-23 18:47:31 arvados.cwl-runner[27368] INFO: Pipeline instance su92l-d1hrv-w30y0vt960e08la
[workflow main-hu34D5B9.cwl] initialized step from file:///home/sguthrie/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow/main-hu34D5B9.cwl
[workflow main-hu34D5B9.cwl] workflow starting
[workflow main-hu34D5B9.cwl] job step file:///home/sguthrie/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow/main-hu34D5B9.cwl#postprocess_alignment not ready
2016-05-23 18:47:31 arvados.cwl-runner[27368] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: <class 'cwltool.errors.WorkflowException'>
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/arvados_cwl/__init__.py", line 711, in arvExecutor
    for runnable in jobiter:
  File "build/bdist.linux-x86_64/egg/cwltool/workflow.py", line 398, in job
    for w in wj.job(builder.job, output_callback, **kwargs):
  File "build/bdist.linux-x86_64/egg/cwltool/workflow.py", line 313, in job
    for newjob in step.iterable:
  File "build/bdist.linux-x86_64/egg/cwltool/workflow.py", line 208, in try_make_job
    inputobj = object_from_state(self.state, inputparms, False, supportsMultipleInput)
  File "build/bdist.linux-x86_64/egg/cwltool/workflow.py", line 123, in object_from_state
    raise WorkflowException(u"Type mismatch between source '%s' (%s) and sink '%s' (%s)" % (src, state[src].parameter["type"], inp["id"], inp["type"]))
WorkflowException: Type mismatch between source 'file:///home/sguthrie/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow/main-hu34D5B9.cwl#rgnames__lb' ({'items': 'null', 'type': 'array'}) and sink 'file:///home/sguthrie/gvcf/sasha/bwa_platypus-yaml/hu34D5B9-workflow/main-hu34D5B9.cwl#alignment.rgnames__lb' ({'items': 'null', 'type': 'array'})
Workflow error, try again with --debug for more information:
  Workflow did not return a result.
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/cwltool/main.py", line 571, in main
    **vars(args))
  File "build/bdist.linux-x86_64/egg/arvados_cwl/__init__.py", line 737, in arvExecutor
    raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
WorkflowException: Workflow did not return a result.

Inputs are in collection https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-ielvi8cl54wso0y