Hi, I could not get the planemo version of VM to work. I was able to load boot drive with image file, but once the VM instance was created, I could never ssh to the server (tried several combinations of ssh keys). (Boot disk 100G and data disk 500G). In the end - I was able to get the ubuntu generic version of VM to work. Does it matter which VM I use? Also, I can run my workflow, and get the output.bedpe - it seems to be formatted ok (although does not match expected results), but during evaluation I get the following error. The command I am running is: ``` SMC-RNA-Challenge/script/dream_runner.py test dryrun1 JAFFA-RNA-Example/workflow/smcFusion-jaffa-workflow.cwl fusion --dir /var/tmp/jaffa/data --cachedir /var/tmp/jaffa/cache/ ``` The error occurs here: ``` job evaluator] Output of job will be cached in /var/tmp/jaffa/cache/d452518acba8de290b4e0515f17b997b [job evaluator] /var/tmp/jaffa/cache/d452518acba8de290b4e0515f17b997b$ docker \ run \ -i \ --volume=/var/tmp/jaffa/data/dryrun1_filtered.bedpe:/var/lib/cwl/stga3b7199e-d40e-4e39-b659-a36bc483b735/dryrun1_filtered.bedpe:ro \ --volume=/home/rebecca_louise_evans/output.bedpe:/var/lib/cwl/stg6894fd5a-8256-4f8f-9932-b30d4c65ea0c/output.bedpe:ro \ --volume=/var/tmp/jaffa/cache/d452518acba8de290b4e0515f17b997b:/var/spool/cwl:rw \ --volume=/tmp/tmp26Esqd:/tmp:rw \ --workdir=/var/spool/cwl \ --read-only=true \ --user=1002 \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/var/spool/cwl \ dreamchallenge/smcrna-functions \ evaluation.py \ evaluateFusionQuant \ --input \ /var/lib/cwl/stg6894fd5a-8256-4f8f-9932-b30d4c65ea0c/output.bedpe \ --truth \ /var/lib/cwl/stga3b7199e-d40e-4e39-b659-a36bc483b735/dryrun1_filtered.bedpe Traceback (most recent call last): File "/opt/SMC-RNA-Challenge/script/../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py", line 166, in sys.exit(main(sys.argv)) File "/opt/SMC-RNA-Challenge/script/../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py", line 156, in main get_truth_values() File "/opt/SMC-RNA-Challenge/script/../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py", line 137, in get_truth_values truth_values.append(string_to_value(truth_bedpe[x][10])) IndexError: list index out of range Command '['/opt/SMC-RNA-Challenge/script/../FusionQuantification/Evaluator/fusionQuantificationEvaluator.py', '-t', '/var/lib/cwl/stga3b7199e-d40e-4e39-b659-a36bc483b735/dryrun1_filtered.bedpe', '-i', '/var/lib/cwl/stg6894fd5a-8256-4f8f-9932-b30d4c65ea0c/output.bedpe']' returned non-zero exit status 1 Error while running job: Error collecting output for parameter 'output': Did not find output file with glob pattern: '['quantification_result.out']' [job evaluator] completed permanentFail Output is missing expected field file:///home/rebecca_louise_evans/SMC-RNA-Challenge/FusionQuantification/cwl/FusionQuantWorkflow.cwl#evaluator/output [step evaluator] completion status is permanentFail Workflow error, try again with --debug for more information: Output for workflow not available Traceback (most recent call last): File "SMC-RNA-Challenge/script/dream_runner.py", line 71, in call_cwl temp = json.loads(output) File "/usr/lib/python2.7/json/__init__.py", line 339, in loads return _default_decoder.decode(s) File "/usr/lib/python2.7/json/decoder.py", line 364, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/lib/python2.7/json/decoder.py", line 382, in raw_decode raise ValueError("No JSON object could be decoded") ValueError: No JSON object could be decoded Unable to call cwltool ```