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PNNL-CompBio / decomprolute

A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
MIT License
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Error running sample prot-deconv.cwl command #171

Closed annapamma closed 3 years ago

annapamma commented 3 years ago

I encountered the following error:

ERROR [job download-prot] Job error:
('Error collecting output for parameter \'matrix\':\n../protData/prot-data-cwl-tool.cwl:36:13: Expression evaluation error:\n../protData/prot-data-cwl-tool.cwl:36:13: Expecting value: line 1 column 1 (char 0)\n../protData/prot-data-cwl-tool.cwl:36:13: script was:\n../protData/prot-data-cwl-tool.cwl:36:13: 01 "use strict";\n../protData/prot-data-cwl-tool.cwl:36:13: 02 var inputs = {\n../protData/prot-data-cwl-tool.cwl:36:13: 03     "cancerType": "hnscc",\n../protData/prot-data-cwl-tool.cwl:36:13: 04     "sampleType": "tumor"\n../protData/prot-data-cwl-tool.cwl:36:13: 05 };\n../protData/prot-data-cwl-tool.cwl:36:13: 06 var self = [];\n../protData/prot-data-cwl-tool.cwl:36:13: 07 var runtime = {\n../protData/prot-data-cwl-tool.cwl:36:13: 08     "cores": 1,\n../protData/prot-data-cwl-tool.cwl:36:13: 09     "ram": 1024,\n../protData/prot-data-cwl-tool.cwl:36:13: 10     "tmpdirSize": 1024,\n../protData/prot-data-cwl-tool.cwl:36:13: 11     "outdirSize": 1024,\n../protData/prot-data-cwl-tool.cwl:36:13: 12     "tmpdir": "/tmp",\n../protData/prot-data-cwl-tool.cwl:36:13: 13     "outdir": "/yDHsnp"\n../protData/prot-data-cwl-tool.cwl:36:13: 14 };\n../protData/prot-data-cwl-tool.cwl:36:13: 15 (function(){\n../protData/prot-data-cwl-tool.cwl:36:13: 16   var name = inputs.cancerType + \'-\' + inputs.sampleType + \'-\' + \'prot-raw.tsv\'\n../protData/prot-data-cwl-tool.cwl:36:13: 17   self[0].basename = name;\n../protData/prot-data-cwl-tool.cwl:36:13: 18   return self[0]\n../protData/prot-data-cwl-tool.cwl:36:13: 19   })()\n../protData/prot-data-cwl-tool.cwl:36:13: stdout was: \'\'\n../protData/prot-data-cwl-tool.cwl:36:13: stderr was: \'evalmachine.<anonymous>:17\n../protData/prot-data-cwl-tool.cwl:36:13:   self[0].basename = name;\n../protData/prot-data-cwl-tool.cwl:36:13:                    ^\n../protData/prot-data-cwl-tool.cwl:36:13: \n../protData/prot-data-cwl-tool.cwl:36:13: TypeError: Cannot set property \'basename\' of undefined\n../protData/prot-data-cwl-tool.cwl:36:13:     at evalmachine.<anonymous>:17:20\n../protData/prot-data-cwl-tool.cwl:36:13:     at evalmachine.<anonymous>:19:5\n../protData/prot-data-cwl-tool.cwl:36:13:     at Script.runInContext (node:vm:142:18)\n../protData/prot-data-cwl-tool.cwl:36:13:     at Script.runInNewContext (node:vm:147:17)\n../protData/prot-data-cwl-tool.cwl:36:13:     at Object.runInNewContext (node:vm:302:38)\n../protData/prot-data-cwl-tool.cwl:36:13:     at Socket.<anonymous> ([eval]:11:57)\n../protData/prot-data-cwl-tool.cwl:36:13:     at Socket.emit (node:events:327:20)\n../protData/prot-data-cwl-tool.cwl:36:13:     at addChunk (node:internal/streams/readable:304:12)\n../protData/prot-data-cwl-tool.cwl:36:13:     at readableAddChunk (node:internal/streams/readable:275:11)\n../protData/prot-data-cwl-tool.cwl:36:13:     at Socket.Readable.push (node:internal/streams/readable:218:10)\'', {})
WARNING [job download-prot] completed permanentFail
ERROR [step download-prot] Output is missing expected field file:///Volumes/Samsung_T3/tumor_deconvolution/proteomicsTumorDeconv/workflows/prot-deconv.cwl#prot-deconv/download-prot/matrix
WARNING [step download-prot] completed permanentFail
INFO [workflow ] completed permanentFail
{
    "deconvoluted": null
}
annapamma commented 3 years ago

@sgosline What version of cwltool are you using? I'll rerun it again with that.

sgosline commented 3 years ago

I'm running 3.0.20201203173111 I have found that sometimes random windows-related carriage returns get added to files (despite my using an ubuntu vm), so that could also be an issue.

annapamma commented 3 years ago

Issue:

docker: Error response from daemon: OCI runtime create failed: invalid mount {Destination:[/tmp] Type:bind Source:/var/lib/docker/volumes/c619639eb5a84b25cfe8911e9eeced8a698d3555abbe5bd931357a146f42977c/_data Options:[rbind]}: mount destination [/tmp] not absolute: unknown.
annapamma commented 3 years ago

Solved by updating to latest Docker images