[DOCKTESTERS] [DOCKTERTERS] Issues with Consensus workflow

[Miguel Vazquez]

Dear all,

I've ran into some more trouble with the Consensus workflow. In particular
its two issues that I'm not sure if they are related.

First of all is that I followed the advice to download the data necessary
before hand:

mkdir dbs
docker run -it -v "${PWD}/dbs":/dbs consensus_call download reference /dbs
docker run -it -v "${PWD}/dbs":/dbs consensus_call download annotations /dbs
docker run -it -v "${PWD}/dbs":/dbs consensus_call download cosmic /dbs

However the last part that download COSMIC give me an error. I tried using
my login email address and password and I get 'Permission denied, please
try again.' I've check COSMIC several times and reset my password. I have
SFTP access enabled and everything. I'm not sure what is happening.

Despite this I though that the workflow might be able to run, since the
COSMIC data is optional, but I get the following error


ubuntu at ip-10-42-6-176:~/DockerTest-Miguel$ cd
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/ && dockstore tool
launch --script --entry quay.io/pancancer/pcawg-consensus-caller:latest
 --json Dockstore.json
Creating directories for run of Dockstore launcher at:
./datastore//launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0
Provisioning your input files to your local machine
Calling out to cwltool to run your tool
Executing: cwltool --enable-dev --non-strict --outdir
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/outputs/
--tmpdir-prefix
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/tmp/
--tmp-outdir-prefix
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/working/
/tmp/1495367250976-0/temp3097766058272663834.cwl
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/workflow_params.json
/usr/local/bin/cwltool 1.0.20161202203310
Resolved '/tmp/1495367250976-0/temp3097766058272663834.cwl' to
'file:///tmp/1495367250976-0/temp3097766058272663834.cwl'
Got workflow error
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 227,
in single_job_executor
    for r in jobiter:
  File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line
370, in job
    j.command_line = flatten(map(builder.generate_arg, builder.bindings))
  File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line
158, in generate_arg
    value = self.do_eval(binding["valueFrom"], context=value)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line
206, in do_eval
    timeout=self.timeout)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
186, in do_eval
    jslib=jslib)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
144, in interpolate
    timeout=timeout)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
127, in evaluator
    return next_seg(m.group(0)[m.end(1) - m.start(0):-1], obj[m.group(1)])
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line
113, in next_seg
    return next_seg(remain[m.end(0):], obj[m.group(0)[1:]])
*KeyError: 'output_file_name'*
*Workflow error, try again with --debug for more information:*
*  'output_file_name'*
org.apache.commons.exec.ExecuteException: Process exited with an error: 1
(Exit value: 1)
        at
org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
        at
org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
        at
org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
        at java.lang.Thread.run(Thread.java:745)
java.lang.RuntimeException: problems running command: cwltool --enable-dev
--non-strict --outdir
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/outputs/
--tmpdir-prefix
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/tmp/
--tmp-outdir-prefix
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/working/
/tmp/1495367250976-0/temp3097766058272663834.cwl
/mnt/1TB/work/DockerTest-Miguel/tests/Consensus/DO52621/./datastore/launcher-92578913-cbbf-4c57-9d19-35b83c4b6fb0/workflow_params.json

Could this be related to the problem with COSMIC?

Best regards

Miguel
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