Hi Michael, Please see below output when using --debug option: sudo cwltool --debug --cachedir /scratch/user/h3abionet16S/cachedir/cache --outdir /scratch/user/h3abionet16S/workflow_output /scratch/user/h3abionet16S/workflows/completeWorkflow.cwl /scratch/user/h3abionet16S/example/input.yml
/usr/local/bin/cwltool 1.0.20161207161158
Resolved '/scratch/user/h3abionet16S/workflows/completeWorkflow.cwl' to 'file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl'
[workflow completeWorkflow.cwl] initialized from file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl
[workflow completeWorkflow.cwl] workflow starting
[workflow completeWorkflow.cwl] job step file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#runFastqc not ready
[workflow completeWorkflow.cwl] job step file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#otuTableToBiom not ready
[workflow completeWorkflow.cwl] job step file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#renameOTU not ready
[workflow completeWorkflow.cwl] job step file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#createSummaryObservations not ready
[workflow completeWorkflow.cwl] starting step arrayOfFilePairsToFileArray
[job step arrayOfFilePairsToFileArray] job input {
"file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#arrayOfFilePairsToFileArray/arrayOfFilePairs": [
{
"reverse": {
"basename": "Dog10_R2.fastq",
"class": "File",
"location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog10_R2.fastq"
},
"barcode_sequence": "NNNNNGTGCCAGCMGCCGCGGTAA",
"treatment": 4,
"sample_id": "Dog10",
"forward": {
"basename": "Dog10_R1.fastq",
"class": "File",
"location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog10_R1.fastq"
},
"linker_primer_sequence": "NNNNNGGACTACHVGGGTWTCTAAT",
"reverse_primer": "NNNNNGGACTACHVGGGTWTCTAAT",
"dog_breed": "K"
},
....
0238 {
0239 "reverse": {
0240 "basename": "Dog8_R2.fastq",
0241 "class": "File",
0242 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog8_R2.fastq"
0243 },
0244 "barcode_sequence": "NNNNNGTGCCAGCMGCCGCGGTTC",
0245 "treatment": 4,
0246 "sample_id": "Dog8",
0247 "forward": {
0248 "basename": "Dog8_R1.fastq",
0249 "class": "File",
0250 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog8_R1.fastq"
0251 },
0252 "linker_primer_sequence": "NNNNNGGACTACHVGGGTWTCTAAT",
0253 "reverse_primer": "NNNNNGGACTACHVGGGTWTCTAAT",
0254 "dog_breed": "B"
0255 },
0256 {
0257 "reverse": {
0258 "basename": "Dog9_R2.fastq",
0259 "class": "File",
0260 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog9_R2.fastq"
0261 },
0262 "barcode_sequence": "NNNNNGTGCCAGCMGCCGCGGTTG",
0263 "treatment": 0,
0264 "sample_id": "Dog9",
0265 "forward": {
0266 "basename": "Dog9_R1.fastq",
0267 "class": "File",
0268 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog9_R1.fastq"
0269 },
0270 "linker_primer_sequence": "NNNNNGGACTACHVGGGTWTCTAAT",
0271 "reverse_primer": "NNNNNGGACTACHVGGGTWTCTAAT",
0272 "dog_breed": "G"
0273 }
0274 ]
0275 };
0276 var self = null;
0277 var runtime = {
0278 "outdirSize": 1024,
0279 "ram": 1024,
0280 "tmpdirSize": 1024,
0281 "cores": 1,
0282 "tmpdir": "/tmp/tmp7vzSIM",
0283 "outdir": "/tmp/tmpVXaRx2"
0284 };
0285 (function(){ var val; var ret = []; for (val of inputs.arrayOfFilePairs) {
0286 ret.push(val.forward);
0287 ret.push(val.reverse);
0288 } return { 'pairByPairs': ret } ; })()
stdout was: ''
stderr was: '
[eval]:10
process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {}))
^
SyntaxError: Unexpected identifier
at Socket.<anonymous> ([eval]:10:55)
at Socket.EventEmitter.emit (events.js:95:17)
at Socket.<anonymous> (_stream_readable.js:746:14)
at Socket.EventEmitter.emit (events.js:92:17)
at emitReadable_ (_stream_readable.js:408:10)
at emitReadable (_stream_readable.js:404:5)
at readableAddChunk (_stream_readable.js:165:9)
at Socket.Readable.push (_stream_readable.js:127:10)
at Pipe.onread (net.js:526:21)
'
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line 55, in run
ev = self.builder.do_eval(self.script)
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 129, in evaluator
return sandboxjs.execjs(ex, jslib, timeout=timeout)
File "/usr/local/lib/python2.7/dist-packages/cwltool/sandboxjs.py", line 137, in execjs
raise JavascriptException(u"Returncode was: %s\nscript was:\n%s\nstdout was: '%s'\nstderr was: '%s'\n" % (nodejs.returncode, fn_linenum(), stdoutdata, stderrdata))
JavascriptException: Returncode was: 8
script was:
0001 "use strict";
0002 var inputs = {
0003 "arrayOfFilePairs": [
0004 {
0005 "reverse": {
0006 "basename": "Dog10_R2.fastq",
0007 "class": "File",
0008 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog10_R2.fastq"
0009 },
0010 "barcode_sequence": "NNNNNGTGCCAGCMGCCGCGGTAA",
0011 "treatment": 4,
0012 "sample_id": "Dog10",
0013 "forward": {
0014 "basename": "Dog10_R1.fastq",
0015 "class": "File",
0016 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog10_R1.fastq"
0017 },
0018 "linker_primer_sequence": "NNNNNGGACTACHVGGGTWTCTAAT",
0019 "reverse_primer": "NNNNNGGACTACHVGGGTWTCTAAT",
0020 "dog_breed": "K"
0021 },
0022 .........
0256 {
0257 "reverse": {
0258 "basename": "Dog9_R2.fastq",
0259 "class": "File",
0260 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog9_R2.fastq"
0261 },
0262 "barcode_sequence": "NNNNNGTGCCAGCMGCCGCGGTTG",
0263 "treatment": 0,
0264 "sample_id": "Dog9",
0265 "forward": {
0266 "basename": "Dog9_R1.fastq",
0267 "class": "File",
0268 "location": "file:///scratch/user/h3abionet16S/example/dog_stool_samples/Dog9_R1.fastq"
0269 },
0270 "linker_primer_sequence": "NNNNNGGACTACHVGGGTWTCTAAT",
0271 "reverse_primer": "NNNNNGGACTACHVGGGTWTCTAAT",
0272 "dog_breed": "G"
0273 }
0274 ]
0275 };
0276 var self = null;
0277 var runtime = {
0278 "outdirSize": 1024,
0279 "ram": 1024,
0280 "tmpdirSize": 1024,
0281 "cores": 1,
0282 "tmpdir": "/tmp/tmp7vzSIM",
0283 "outdir": "/tmp/tmpVXaRx2"
0284 };
0285 (function(){ var val; var ret = []; for (val of inputs.arrayOfFilePairs) {
0286 ret.push(val.forward);
0287 ret.push(val.reverse);
0288 } return { 'pairByPairs': ret } ; })()
stdout was: ''
stderr was: '
[eval]:10
process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {}))
^
SyntaxError: Unexpected identifier
at Socket.<anonymous> ([eval]:10:55)
at Socket.EventEmitter.emit (events.js:95:17)
at Socket.<anonymous> (_stream_readable.js:746:14)
at Socket.EventEmitter.emit (events.js:92:17)
at emitReadable_ (_stream_readable.js:408:10)
at emitReadable (_stream_readable.js:404:5)
at readableAddChunk (_stream_readable.js:165:9)
at Socket.Readable.push (_stream_readable.js:127:10)
at Pipe.onread (net.js:526:21)
'
Output is missing expected field file:///scratch/user/h3abionet16S/workflows/completeWorkflow.cwl#arrayOfFilePairsToFileArray/pairByPairs
[step arrayOfFilePairsToFileArray] produced output {}
[step arrayOfFilePairsToFileArray] completion status is permanentFail
Workflow error, try again with --debug for more information:
Output for workflow not available
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 714, in main
**vars(args))
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/workflow.py", line 420, in job
for w in wj.job(builder.job, output_callback, **kwargs):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 391, in job
raise WorkflowException("Output for workflow not available")
WorkflowException: Output for workflow not available
•
written
by
Shakuntala Baichoo •
Version 0.10.25 is too old of a version of node, you will need to upgrade
For example, my system is running 4.6.1.
Checking http://packages.ubuntu.com/search?keywords=nodejs I would guess that you're in an Ubuntu Trusty (14.04LTS) virtual machine -- being two years old would explain the issue :-)
I recommend upgrading to an Ubuntu Xenial (16.04LTS) virtual machine.
I've created an issue on the CWL reference implementation GitHub repository to remind us to produce a better error message in the future: https://github.com/common-workflow-language/cwltool/issues/254
nodejs --version
v0.10.25
node --version
The program 'node' can be found in the following packages:
* node
* nodejs-legacy
Try: sudo apt-get install <selected package>
Funny, the second one. I guess that is causing the problem.
Hi Michael! Thank you very much.
Best Regards Shakun
You are very welcome and thank you for using biostars for asking your question.
A few tips: It is polite to respond using the 'add comment' button instead of creating a new "Answer" to a question.
Also it would be useful to "accept" my response using the checkmark-in-a-circle button next to it.
Finally, no need to begin your question with: "Hi Michael", as there are other people who can answer CWL related questions :-)
Thank you.
Will do as per your advice, next time.
Best Regards Shakun
Log in to answer this question.
Huh, I though the --debug would have output the version of nodejs being used.
What's the output of
and
on your virtual machine?
Hi! The answers are:
nodejs --version v0.10.25
node --version The program 'node' can be found in the following packages: * node * nodejs-legacy Try: sudo apt-get install <selected package="">
I guess the second one is the problem!
Best Regards
Shakun
CWLtool checks for either name, so that isn't the problem