[DOCKTESTERS] [DOCKTERTERS] Issues with Consensus workflow
Solomon Shorser
solomon.shorser at oicr.on.ca
Tue May 23 10:28:15 EDT 2017
Hi Miguel,
I am not sure about the COSMIC error. Did it prompt you for your
username and password? Are you able to access the files with sftp
/outside/ of a docker-container context? I was not the author of this
docker image or the scripts within, but I can talk to the original
author if we cannot solve this ourselves.
As for the CWLTool error:
This error:
||
|*KeyError: 'output_file_name'*|
|
*Workflow error, try again with --debug for more information:*
*'output_file_name'*
|
...suggests that the variable named "output_file_name" was missing,
probably from the input json "workflow_params.json".
If your workflow_params.json file does not have an "output_file_name",
please try adding one (it should look like:
..."output_file_name":"myConsensus.vcf",... in JSON) to the
workflow_params.json file, and let me know how that works.
Thanks,
Solomon Shorser.
On 2017-05-21 07:45 AM, Miguel Vazquez wrote:
> 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
> <http://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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*Solomon Shorser*
Software Developer
*Ontario Institute for Cancer Research*
MaRS Centre
661 University Avenue
Suite 510
Toronto, Ontario
Canada M5G 0A3
Email: solomon.shorser at oicr.on.ca
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Toll-free: 1-866-678-6427
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