This thread is the designated place to ask questions about running the **gdc_dnaseq_transform** workflow.
Created by James Eddy jaeddy Hi @bernest,
I apologize ? this was entirely due to a bug on the validation EC2 instance (which, unfortunately, was creating an error in a place that did not signal the system to notify me as well). I fixed the error, reset your "invalid" submissions, and they're now listed in the validated submissions table.
Note: this error affected submissions between 12/6 and 12/8 to the following workflows (cc: @slagelwa @benstory, whose submissions were also erroneously invalidated):
+ gdc_dnaseq_transform
+ biowardrobe_chipseq_se
+ pcawg-delly-sv-caller
+ pcawg-bwa-mem-aligner
I've reset invalidated submissions for all of these workflows, and everything should hopefully show up as validated shortly!
Sorry again for any confusion or extra work this caused! If there are any duplicated submissions that you would like to remove, let me know.
Best,
James
Hi Jeremiah and James,
I've run the gdc_dnaseq_transform workflow multiple times and each time the checker says it ran successfully, but when I submit it to the challenge it fails. Any ideas? I've pasted my software versions and environment below. I would show my steps, but they're exactly as you described. The only apparent difference is that you ran yours in an EC2 instance, whereas I'm running mine in Linux CentOS. I've seen other successful submissions that seem to deviate more from your example than I have. Thanks. --Ben.
#### Software and environment
Linux
```shell
$ lsb_release -a
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.3.1611 (Core)
Release: 7.3.1611
Codename: Core
```
docker
```shell
$ docker --version
Docker version 17.06.0-ce, build 02c1d87
```
mkvirtualenv
```shell
$ mkvirtualenv --version
15.1.0
```
pip
```shell
$ pip --version
pip 9.0.1 from /usr/lib/python2.7/site-packages (python 2.7)
```
schema
```shell
$ schema-salad-tool schema --version
/usr/bin/schema-salad-tool 2.2.20170222151604
```
cwltool
```shell
$ cwltool --version
/usr/bin/cwltool 1.0.20170217172322
```
synapseClient
```shell
$ synapse --version
Synapse Client 1.7.2
```
Hi,
I am trying to run gdc_dnaseq_transform workflow with `toil`. I have downloaded the files successfully.
```shell
cwltoil --workDir ~/tmp/ dockstore-tool-synapse-get.cwl gdc_dnaseq_transform_get.cwl.json
```
Now when I tried to run the workflow with following command:
```shell
cwltoil --workDir ~/tmp/ cwl/workflows/dnaseq/transform.cwl transform.cwl.json
```
ended up the error message:
```
[STDOUT]
=========> Failed job 'file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/gdc_dnaseq_transform/cwl/tools/decider_bwa_expression.cwl' S/m/job1LNoas
---TOIL WORKER OUTPUT LOG---
INFO:toil:Running Toil version 3.11.0-ca24899f31a2d7f8b3f766a1c99c982ccf1044eb.
INFO:toil.fileStore:Starting job ('file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/gdc_dnaseq_transform/cwl/tools/decider_bwa_expression.cwl' S/m/job1LNoas) with ID (e5473b82ce4039dfe39fa4a02f5e5e2966ac6197).
Failed to evaluate expression:
Expression evaluation error:
evalmachine.:71
exit()
^
ReferenceError: exit is not defined
at get_slice_number (evalmachine.:71:8)
at evalmachine.:81:25
at evalmachine.:99:4
at ContextifyScript.Script.runInContext (vm.js:53:29)
at ContextifyScript.Script.runInNewContext (vm.js:59:15)
at Object.runInNewContext (vm.js:112:38)
at Socket. ([eval]:10:55)
at emitOne (events.js:115:13)
at Socket.emit (events.js:210:7)
at addChunk (_stream_readable.js:266:12)
WARNING:cwltool:Failed to evaluate expression:
Expression evaluation error:
evalmachine.:71
exit()
^
ReferenceError: exit is not defined
at get_slice_number (evalmachine.:71:8)
at evalmachine.:81:25
at evalmachine.:99:4
at ContextifyScript.Script.runInContext (vm.js:53:29)
at ContextifyScript.Script.runInNewContext (vm.js:59:15)
at Object.runInNewContext (vm.js:112:38)
at Socket. ([eval]:10:55)
at emitOne (events.js:115:13)
at Socket.emit (events.js:210:7)
at addChunk (_stream_readable.js:266:12)
Traceback (most recent call last):
File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/worker.py", line 313, in main
job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/job.py", line 1299, in _runner
returnValues = self._run(jobGraph, fileStore)
File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/job.py", line 1244, in _run
return self.run(fileStore)
File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 451, in run
raise cwltool.errors.WorkflowException(status)
WorkflowException: permanentFail
ERROR:toil.worker:Exiting the worker because of a failed job on host YYY
WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/gdc_dnaseq_transform/cwl/tools/decider_bwa_expression.cwl' S/m/job1LNoas with ID S/m/job1LNoas to 0
```
Have you seen something like before? I am running cwltoil version `3.11.0`. Please let me know if you need any additional information from my side to debug the issue.
Thank you very much for providing the workflow!
Cheers!
Vipin
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