output from https://github.com/common-workflow-language/common-workflow-language/issues/139

initial-report

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ sudo
./lobSTR-workflow.cwl lobSTR-demo.json
/usr/local/bin/cwl-runner 1.0.20150929170517
Unhandled exception
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 202, in try_make_job
    for j in jobs:
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 126, in job
    for j in self.step.job(joborder, basedir, output_callback, **kwargs):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 407, in job
    for t in self.embedded_tool.job(joborder, basedir,
functools.partial(self.receive_output, output_callback), **kwargs):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py",
line 67, in job
    builder = self._init_job(joborder, input_basedir, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/process.py",
line 168, in _init_job
    builder.bindings.extend(builder.bind_input(self.inputs_record_schema,
builder.job))
  File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py",
line 58, in bind_input
    bindings.extend(self.bind_input(f, datum[f["name"]],
lead_pos=lead_pos, tail_pos=f["name"]))
  File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py",
line 94, in bind_input
    sfpath = self.do_eval(sf, context=datum["path"])
  File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py",
line 159, in do_eval
    return expression.do_eval(ex, self.job, self.requirements,
self.outdir, self.tmpdir, context=context, pull_image=pull_image)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py",
line 77, in do_eval
    return exeval(ex, jobinput, requirements, outdir, tmpdir, context,
pull_image)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py",
line 36, in exeval
    img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)
  File "/usr/local/lib/python2.7/dist-packages/cwltool/docker.py",
line 98, in get_from_requirements
    raise process.WorkflowException("Docker image %s not found" %
r["dockerImageId"])
WorkflowException: Docker image commonworkflowlanguage/nodejs-engine not found
Got workflow error

new-problem

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ sudo cwltool --debug lobSTR-workflow.cwl lobSTR-demo.json
/usr/local/bin/cwltool 1.0.20150929170517
[workflow 140692731877200] initialized from file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl
[workflow 140692731877200] starting
[workflow 140692731877200] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samindex not ready
[workflow 140692731877200] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#allelotype not ready
[workflow 140692731877200] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samsort not ready
[step 140692726602000] starting job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR of workflow 140692731877200
Invoking expression engine ['docker', 'run', '-i', '--rm', 'commonworkflowlanguage/nodejs-engine', 'cwlNodeEngine.js'] with {
"script": "[{\"path\": $self.replace(/(.)ref\.fasta/, \"$1chromsizes.tab\"), \"class\": \"File\"},\n {\"path\": $self.replace(/(.)ref\.fasta/, \"$1mergedref.bed\"), \"class\": \"File\"},\n {\"path\": $self.replace(/(.)ref\.fasta/, \"$1ref_map.tab\"), \"class\": \"File\"}]\n", 
"job": {
"files": null, 
"minflank": 8, 
"reference": {
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}
]
}, 
"min-read-length": 45, 
"min-flank-allow-mismatch": 30, 
"rg-lib": "mylib", 
"max-read-length": 1024, 
"output_prefix": "demo", 
"max-hits-quit-aln": 1000, 
"maq": 100, 
"fft-window-step": 4, 
"extend": 1000, 
"mismatch": 1, 
"max-diff-ref": 50, 
"maxflank": 100, 
"e": 1, 
"p2": [
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_2.fq", 
"class": "File"
}
], 
"p1": [
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_1.fq", 
"class": "File"
}
], 
"entropy-threshold": 0.45, 
"g": 1, 
"fft-window-size": 16, 
"r": -1, 
"rg-sample": "mysample"
}, 
"context": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"engineConfig": [], 
"tmpdir": "/tmp/job_tmp", 
"outdir": "/tmp/job_output"
}
[job 140692726600656] initializing from file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-tool.cwl as part of step 140692726602000
[job 140692726600656] {
"p2": [
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_2.fq", 
"class": "File"
}
], 
"p1": [
{
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_1.fq", 
"class": "File"
}
], 
"rg-lib": "mylib", 
"reference": {
"path": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File"
}, 
"output_prefix": "demo", 
"rg-sample": "mysample"
}
[job 140692726600656] command line bindings is [
{
"position": [
-1000000, 
0
], 
"valueFrom": "lobSTR"
}, 
{
"position": [
0, 
0
], 
"valueFrom": "--verbose"
}, 
{
"position": [
0, 
1
], 
"valueFrom": "--noweb"
}, 
{
"position": [
0, 
2
], 
"valueFrom": null, 
"do_eval": {
"engine": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/node-engine.cwl", 
"script": "{\n var r = /.(\.fastq|\.fq)(\.gz)?$/i;\n var m;\n if ($job['files']) {\n m = r.exec($job.files[0].path);\n } else {\n m = r.exec($job.p1[0].path);\n }\n if (m) {\n if (m[2]) {\n return [\"--fastq\", \"--gzip\"];\n } else {\n return \"--fastq\";\n }\n } else {\n return null;\n }\n}\n"
}
}, 
{
"position": [
0, 
3
], 
"valueFrom": null, 
"do_eval": {
"engine": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/node-engine.cwl", 
"script": "{\n if ($job['files'] && (/.\.bam$/i).test($job.files[0].path) && !$job.bampair) {\n return \"--bam\";\n } else {\n return null;\n }\n}\n"
}
}, 
{
"position": [
0, 
"e"
], 
"prefix": "-e", 
"valueFrom": 1
}, 
{
"position": [
0, 
"entropy-threshold"
], 
"prefix": "--entropy-threshold", 
"valueFrom": 0.45
}, 
{
"position": [
0, 
"extend"
], 
"prefix": "--extend", 
"valueFrom": 1000
}, 
{
"position": [
0, 
"fft-window-size"
], 
"prefix": "--fft-window-size", 
"valueFrom": 16
}, 
{
"position": [
0, 
"fft-window-step"
], 
"prefix": "--fft-window-step", 
"valueFrom": 4
}, 
{
"position": [
0, 
"g"
], 
"prefix": "-g", 
"valueFrom": 1
}, 
{
"position": [
0, 
"maq"
], 
"prefix": "--mapq", 
"valueFrom": 100
}, 
{
"position": [
0, 
"max-diff-ref"
], 
"prefix": "--max-diff-ref", 
"valueFrom": 50
}, 
{
"position": [
0, 
"max-hits-quit-aln"
], 
"prefix": "--max-hits-quit-aln", 
"valueFrom": 1000
}, 
{
"position": [
0, 
"max-read-length"
], 
"prefix": "--min-read-length", 
"valueFrom": 1024
}, 
{
"position": [
0, 
"maxflank"
], 
"prefix": "--maxflank", 
"valueFrom": 100
}, 
{
"position": [
0, 
"min-flank-allow-mismatch"
], 
"prefix": "--min-flank-allow-mismatch", 
"valueFrom": 30
}, 
{
"position": [
0, 
"min-read-length"
], 
"prefix": "--min-read-length", 
"valueFrom": 45
}, 
{
"position": [
0, 
"minflank"
], 
"prefix": "--minflank", 
"valueFrom": 8
}, 
{
"position": [
0, 
"mismatch"
], 
"prefix": "--mismatch", 
"valueFrom": 1
}, 
{
"position": [
0, 
"output_prefix"
], 
"prefix": "--out", 
"valueFrom": "demo"
}, 
{
"position": [
0, 
"r"
], 
"prefix": "-e", 
"valueFrom": -1
}, 
{
"secondaryFiles": [
".amb", 
".ann", 
".bwt", 
".pac", 
".rbwt", 
".rpac", 
".rsa", 
".sa", 
{
"engine": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/node-engine.cwl", 
"script": "[{\"path\": $self.replace(/(.)ref\.fasta/, \"$1chromsizes.tab\"), \"class\": \"File\"},\n {\"path\": $self.replace(/(.)ref\.fasta/, \"$1mergedref.bed\"), \"class\": \"File\"},\n {\"path\": $self.replace(/(.)ref\.fasta/, \"$1ref_map.tab\"), \"class\": \"File\"}]\n"
}
], 
"prefix": "--index-prefix", 
"do_eval": {
"engine": "file:///home/rgiuly/cwl-workflows/workflows/lobSTR/node-engine.cwl", 
"script": "{ return {\"path\": $self.path.match(/(.)ref\.fasta/)[1], \"class\": \"File\"}; }\n"
}, 
"valueFrom": {
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab", 
"class": "File"
}
]
}, 
"position": [
0, 
"reference"
]
}, 
{
"position": [
0, 
"rg-lib"
], 
"prefix": "--rg-lib", 
"valueFrom": "mylib"
}, 
{
"position": [
0, 
"rg-sample"
], 
"prefix": "--rg-sample", 
"valueFrom": "mysample"
}, 
{
"position": [
2, 
"p1"
], 
"prefix": "--p1", 
"itemSeparator": ",", 
"valueFrom": [
{
"path": "/tmp/job867057915_lobSTR/tmp_1.fq", 
"class": "File"
}
]
}, 
{
"position": [
3, 
"p2"
], 
"prefix": "--p2", 
"itemSeparator": ",", 
"valueFrom": [
{
"path": "/tmp/job867057915_lobSTR/tmp_2.fq", 
"class": "File"
}
]
}
]
[job 140692726600656] path mappings is {
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_1.fq": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_1.fq", 
"/tmp/job867057915_lobSTR/tmp_1.fq"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa",
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_2.fq": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/tmp_2.fq", 
"/tmp/job867057915_lobSTR/tmp_2.fq"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab",
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt",
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt"
], 
"file:///home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt": [
"/home/rgiuly/cwl-workflows/workflows/lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt"
]
}
Invoking expression engine ['docker', 'run', '-i', '--rm', 'commonworkflowlanguage/nodejs-engine', 'cwlNodeEngine.js'] with {
"script": "{\n var r = /.(\.fastq|\.fq)(\.gz)?$/i;\n var m;\n if ($job['files']) {\n m = r.exec($job.files[0].path);\n } else {\n m = r.exec($job.p1[0].path);\n }\n if (m) {\n if (m[2]) {\n return [\"--fastq\", \"--gzip\"];\n } else {\n return \"--fastq\";\n }\n } else {\n return null;\n }\n}\n", 
"job": {
"files": null, 
"minflank": 8, 
"bampair": null, 
"reference": {
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab", 
"class": "File"
}
]
}, 
"min-read-length": 45, 
"bwaq": null, 
"min-flank-allow-mismatch": 30, 
"rg-lib": "mylib", 
"max-read-length": 1024, 
"output_prefix": "demo", 
"max-hits-quit-aln": 1000, 
"maq": 100, 
"fft-window-step": 4, 
"extend": 1000, 
"mismatch": 1, 
"max-diff-ref": 50, 
"oldillumina": null, 
"maxflank": 100, 
"e": 1, 
"p2": [
{
"path": "/tmp/job867057915_lobSTR/tmp_2.fq", 
"class": "File"
}
], 
"multi": null, 
"p1": [
{
"path": "/tmp/job867057915_lobSTR/tmp_1.fq", 
"class": "File"
}
], 
"entropy-threshold": 0.45, 
"g": 1, 
"fft-window-size": 16, 
"r": -1, 
"u": null, 
"rg-sample": "mysample"
}, 
"context": null, 
"engineConfig": [], 
"tmpdir": "/tmp/job_tmp", 
"outdir": "/tmp/job_output"
}
Invoking expression engine ['docker', 'run', '-i', '--rm', 'commonworkflowlanguage/nodejs-engine', 'cwlNodeEngine.js'] with {
"script": "{\n if ($job['files'] && (/.\.bam$/i).test($job.files[0].path) && !$job.bampair) {\n return \"--bam\";\n } else {\n return null;\n }\n}\n", 
"job": {
"files": null, 
"minflank": 8, 
"bampair": null, 
"reference": {
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab", 
"class": "File"
}
]
}, 
"min-read-length": 45, 
"bwaq": null, 
"min-flank-allow-mismatch": 30, 
"rg-lib": "mylib", 
"max-read-length": 1024, 
"output_prefix": "demo", 
"max-hits-quit-aln": 1000, 
"maq": 100, 
"fft-window-step": 4, 
"extend": 1000, 
"mismatch": 1, 
"max-diff-ref": 50, 
"oldillumina": null, 
"maxflank": 100, 
"e": 1, 
"p2": [
{
"path": "/tmp/job867057915_lobSTR/tmp_2.fq", 
"class": "File"
}
], 
"multi": null, 
"p1": [
{
"path": "/tmp/job867057915_lobSTR/tmp_1.fq", 
"class": "File"
}
], 
"entropy-threshold": 0.45, 
"g": 1, 
"fft-window-size": 16, 
"r": -1, 
"u": null, 
"rg-sample": "mysample"
}, 
"context": null, 
"engineConfig": [], 
"tmpdir": "/tmp/job_tmp", 
"outdir": "/tmp/job_output"
}
Invoking expression engine ['docker', 'run', '-i', '--rm', 'commonworkflowlanguage/nodejs-engine', 'cwlNodeEngine.js'] with {
"script": "{ return {\"path\": $self.path.match(/(.)ref\.fasta/)[1], \"class\": \"File\"}; }\n", 
"job": {
"files": null, 
"minflank": 8, 
"bampair": null, 
"reference": {
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab", 
"class": "File"
}
]
}, 
"min-read-length": 45, 
"bwaq": null, 
"min-flank-allow-mismatch": 30, 
"rg-lib": "mylib", 
"max-read-length": 1024, 
"output_prefix": "demo", 
"max-hits-quit-aln": 1000, 
"maq": 100, 
"fft-window-step": 4, 
"extend": 1000, 
"mismatch": 1, 
"max-diff-ref": 50, 
"oldillumina": null, 
"maxflank": 100, 
"e": 1, 
"p2": [
{
"path": "/tmp/job867057915_lobSTR/tmp_2.fq", 
"class": "File"
}
], 
"multi": null, 
"p1": [
{
"path": "/tmp/job867057915_lobSTR/tmp_1.fq", 
"class": "File"
}
], 
"entropy-threshold": 0.45, 
"g": 1, 
"fft-window-size": 16, 
"r": -1, 
"u": null, 
"rg-sample": "mysample"
}, 
"context": {
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta", 
"class": "File", 
"secondaryFiles": [
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.amb", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.ann", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.bwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.pac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rbwt", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rpac", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.rsa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta.sa", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_chromsizes.tab", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_mergedref.bed", 
"class": "File"
}, 
{
"path": "/tmp/job867057915_lobSTR/hg19_v3.0.2/lobstr_v3.0.2_hg19_ref/lobSTR_ref_map.tab", 
"class": "File"
}
]
}, 
"engineConfig": [], 
"tmpdir": "/tmp/job_tmp", 
"outdir": "/tmp/job_output"
}
['docker', 'load']
Sending GET request to https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-x2ae13tsx5jqg8d/1nduktd8dpvhdpgsva82lje0i710kgzb6rttks5jldx7s2y7k9/7e0c0ae3bf4e70442f9b8eee816ec23426d9e1169a2925316e5c932745e21613.tar
Got workflow error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 152, in single_job_executor
r.run(*kwargs)
File "/usr/local/lib/python2.7/dist-packages/cwltool/job.py", line 56, in run
img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/docker.py", line 94, in get_from_requirements
if get_image(r, pull_image, dry_run):
File "/usr/local/lib/python2.7/dist-packages/cwltool/docker.py", line 58, in get_image
req = requests.get(dockerRequirement["dockerLoad"], stream=True)
File "/usr/local/lib/python2.7/dist-packages/requests/api.py", line 69, in get
return request('get', url, params=params, *kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/api.py", line 50, in request
response = session.request(method=method, url=url, *kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 471, in request
resp = self.send(prep, *send_kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/sessions.py", line 579, in send
r = adapter.send(request, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/requests/adapters.py", line 430, in send
raise SSLError(e, request=request)
SSLError: hostname 'workbench.qr1hi.arvadosapi.com' doesn't match either of 'cloud.curoverse.com', 'curoverse.com'
Workflow error:
hostname 'workbench.qr1hi.arvadosapi.com' doesn't match either of 'cloud.curoverse.com', 'curoverse.com'
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 411, in main
move_outputs=args.move_outputs
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 157, in single_job_executor
raise workflow.WorkflowException("%s" % e, )
WorkflowException: hostname 'workbench.qr1hi.arvadosapi.com' doesn't match either of 'cloud.curoverse.com', 'curoverse.com'
FATA[0000] Error: EOF

with-and-without-sudo

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ sudo cwltool --debug lobSTR-workflow.cwl lobSTR-demo.json 
/usr/local/bin/cwltool 1.0.20150929170517
[workflow 140503609669456] initialized from file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl
[workflow 140503609669456] starting
[step 140503603535824] starting job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR of workflow 140503609669456
Unhandled exception
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 202, in try_make_job
for j in jobs:
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 126, in job
for j in self.step.job(joborder, basedir, output_callback, *kwargs):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 407, in job
for t in self.embedded_tool.job(joborder, basedir, functools.partial(self.receive_output, output_callback), *kwargs):
File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line 67, in job
builder = self._init_job(joborder, input_basedir, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/cwltool/process.py", line 168, in _init_job
builder.bindings.extend(builder.bind_input(self.inputs_record_schema, builder.job))
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 58, in bind_input
bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"]))
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 94, in bind_input
sfpath = self.do_eval(sf, context=datum["path"])
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 159, in do_eval
return expression.do_eval(ex, self.job, self.requirements, self.outdir, self.tmpdir, context=context, pull_image=pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line 77, in do_eval
return exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line 36, in exeval
img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/docker.py", line 98, in get_from_requirements
raise process.WorkflowException("Docker image %s not found" % r["dockerImageId"])
WorkflowException: Docker image commonworkflowlanguage/nodejs-engine not found
[workflow 140503609669456] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#allelotype not ready
[workflow 140503609669456] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samindex not ready
[workflow 140503609669456] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samsort not ready
Got workflow error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 154, in single_job_executor
raise workflow.WorkflowException("Workflow cannot make any more progress.")
WorkflowException: Workflow cannot make any more progress.
Workflow error:
Workflow cannot make any more progress.
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 411, in main
move_outputs=args.move_outputs
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 157, in single_job_executor
raise workflow.WorkflowException("%s" % e, )
WorkflowException: Workflow cannot make any more progress.
rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$

Also just FYI, without sudo, I get this:

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ cwltool --debug lobSTR-workflow.cwl lobSTR-demo.json 
/usr/local/bin/cwltool 1.0.20150929170517
[workflow 139764783942928] initialized from file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl
[workflow 139764783942928] starting
[workflow 139764783942928] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samindex not ready
[workflow 139764783942928] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#allelotype not ready
[step 139764783044752] starting job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#lobSTR of workflow 139764783942928
time="2015-10-07T11:48:11-07:00" level=fatal msg="Get http:///var/run/docker.sock/v1.17/version: dial unix /var/run/docker.sock: permission denied. Are you trying to connect to a TLS-enabled daemon without TLS?" 
Unhandled exception
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 202, in try_make_job
for j in jobs:
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 126, in job
for j in self.step.job(joborder, basedir, output_callback, *kwargs):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 407, in job
for t in self.embedded_tool.job(joborder, basedir, functools.partial(self.receive_output, output_callback), *kwargs):
File "/usr/local/lib/python2.7/dist-packages/cwltool/draft2tool.py", line 67, in job
builder = self._init_job(joborder, input_basedir, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/cwltool/process.py", line 168, in _init_job
builder.bindings.extend(builder.bind_input(self.inputs_record_schema, builder.job))
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 58, in bind_input
bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"]))
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 94, in bind_input
sfpath = self.do_eval(sf, context=datum["path"])
File "/usr/local/lib/python2.7/dist-packages/cwltool/builder.py", line 159, in do_eval
return expression.do_eval(ex, self.job, self.requirements, self.outdir, self.tmpdir, context=context, pull_image=pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line 77, in do_eval
return exeval(ex, jobinput, requirements, outdir, tmpdir, context, pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/expression.py", line 36, in exeval
img_id = docker.get_from_requirements(docker_req, docker_is_req, pull_image)
File "/usr/local/lib/python2.7/dist-packages/cwltool/docker.py", line 90, in get_from_requirements
raise process.WorkflowException(errmsg)
WorkflowException: Cannot communicate with docker daemon: Command '['docker', 'version']' returned non-zero exit status 1
[workflow 139764783942928] job step file:///home/rgiuly/cwl-workflows/workflows/lobSTR/lobSTR-workflow.cwl#samsort not ready
Got workflow error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 154, in single_job_executor
raise workflow.WorkflowException("Workflow cannot make any more progress.")
WorkflowException: Workflow cannot make any more progress.
Workflow error:
Workflow cannot make any more progress.
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 411, in main
move_outputs=args.move_outputs
File "/usr/local/lib/python2.7/dist-packages/cwltool/main.py", line 157, in single_job_executor
raise workflow.WorkflowException("%s" % e, )
WorkflowException: Workflow cannot make any more progress.
rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$