Bug #9659
Updated by Brett Smith almost 8 years ago
It appears that the cwl documentation may be out of sync with latest arvados-cwl-runner code updates. <pre>$ arvados-cwl-runner --debug bwa-mem.cwl bwa-mem-input.yml /data/scratch/brett/cwl/bin/arvados-cwl-runner 1.0.20160717133709, arvados-python-client 0.1.20160721023501, 0.1.20160627200331, cwltool 1.0.20160714182449 2016-07-26 19:02:49 arvados.arv-run[43558] 20:44:32 arvados.arv-run[29762] INFO: Upload local files: "bwa-mem.cwl" 2016-07-26 19:02:50 arvados.arv-run[43558] 20:44:33 arvados.arv-run[29762] INFO: Uploaded to qr1hi-4zz18-yyrz0vbtn8iuuif qr1hi-4zz18-rbnsxtxmyjshh87 2016-07-26 19:02:59 arvados.cwl-runner[43558] INFO: Submitted job qr1hi-8i9sb-vvdfe70pw0oucch 20:44:33 arvados.cwl-runner[29762] ERROR: Caught unhandled exception, marking pipeline as failed. Error was: 'UploadFile' object has no attribute 'keepref' 2016-07-26 19:03:06 arvados.cwl-runner[43558] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-vvdfe70pw0oucch) is Running 2016-07-26 19:03:21 arvados.cwl-runner[43558] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-vvdfe70pw0oucch) is Failed 2016-07-26 19:03:21 arvados.cwl-runner[43558] ERROR: While getting final output object: [Errno 2] Traceback (most recent call last): File not found "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/__init__.py", line 190, in arvExecutor runnable.run(**kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/arvjob.py", line 216, in run job_spec = self.arvados_job_spec(*args, **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/arvjob.py", line 202, in arvados_job_spec workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/runner.py", line 85, in arvados_job_spec **kwargs) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 26, in __init__ super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/cwltool/pathmapper.py", line 90, in __init__ self.setup(referenced_files, basedir) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 92, in setup self._pathmap[src] = MapperEnt("keep:" + st.keepref, st.fn, "File") 2016-07-26 19:03:21 arvados.cwl-runner[43558] WARNING: Overall process status is permanentFail AttributeError: 'UploadFile' object has no attribute 'keepref' Workflow error, try again with --debug for more information: Workflow failed. Traceback (most recent call last): File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/cwltool/main.py", line 707, in main **vars(args)) File "/data/scratch/brett/cwl/local/lib/python2.7/site-packages/arvados_cwl/__init__.py", line 222, in arvExecutor raise WorkflowException("Workflow failed.") WorkflowException: Workflow failed. </pre> This error occurs consistently whether or not I use @--debug@.