Dear Organizers,
I got this log file when we uploaded the results.
submission ID 9713889
Please, could you tell me any solution of this error?
Thank you, we appreciate your help.
STDERR: 2021-08-10T08:31:19.408998532Z b8965e4da00e 2021-08-10 08:31:19,408 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d8daeca3-4ead-45f5-9c65-059f2a42be7e/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d8daeca3-4ead-45f5-9c65-059f2a42be7e/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-10T08:31:52.636580926Z Traceback (most recent call last):
STDERR: 2021-08-10T08:31:52.636609555Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2021-08-10T08:31:52.636613285Z sys.exit(main())
STDERR: 2021-08-10T08:31:52.636615723Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1587, in main
STDERR: 2021-08-10T08:31:52.636618311Z loading_context, uri = cwltool.load_tool.resolve_and_validate_document(loading_context, workflowobj, uri)
STDERR: 2021-08-10T08:31:52.636620696Z File "/usr/local/lib/python3.6/site-packages/cwltool/load_tool.py", line 336, in resolve_and_validate_document
STDERR: 2021-08-10T08:31:52.636623286Z document_loader.resolve_all(workflowobj, fileuri)
STDERR: 2021-08-10T08:31:52.636625449Z File "/usr/local/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1196, in resolve_all
STDERR: 2021-08-10T08:31:52.636627753Z strict_foreign_properties=strict_foreign_properties,
STDERR: 2021-08-10T08:31:52.636629925Z File "/usr/local/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1422, in validate_links
STDERR: 2021-08-10T08:31:52.636632347Z raise errors[0]
STDERR: 2021-08-10T08:31:52.636634471Z schema_salad.exceptions.ValidationException: brats-dream-challenge-infra-main/validation-phase-workflow.cwl:32:1: checking field `steps`
STDERR: 2021-08-10T08:31:52.636636802Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:34:3: checking object
STDERR: 2021-08-10T08:31:52.636639160Z `brats-dream-challenge-infra-main/validation-phase-workflow.cwl#set_submitter_folder_permissions`
STDERR: 2021-08-10T08:31:52.636641696Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:35:5: Field `run` contains
STDERR: 2021-08-10T08:31:52.636643912Z undefined reference to
STDERR: 2021-08-10T08:31:52.636646166Z `https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl`
Created by Juan Pablo Serrano-Rubio TecnmGTO Thank you for the help. Dear @TecnmGTO ,
Thank you for participating!
Apologies, there was a temporary issue with the connection to GitHub, so the workflow had errored out. That said, I did look into your team's submission (ID 9713889) and it is considered invalid as it is not a tarball or zipped archive of NIfTI files.
Hope this helps!