Hello,
I got this traceback, how to solve it?
STDERR: 2021-08-11T05:18:29.645013454Z 32560f633006 2021-08-11 05:18:29,644 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-11T05:18:30.866753736Z Traceback (most recent call last):
STDERR: 2021-08-11T05:18:30.866790998Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2021-08-11T05:18:30.866795763Z sys.exit(main())
STDERR: 2021-08-11T05:18:30.866799042Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1587, in main
STDERR: 2021-08-11T05:18:30.866802249Z loading_context, uri = cwltool.load_tool.resolve_and_validate_document(loading_context, workflowobj, uri)
STDERR: 2021-08-11T05:18:30.866805609Z File "/usr/local/lib/python3.6/site-packages/cwltool/load_tool.py", line 336, in resolve_and_validate_document
STDERR: 2021-08-11T05:18:30.866809263Z document_loader.resolve_all(workflowobj, fileuri)
STDERR: 2021-08-11T05:18:30.866812699Z File "/usr/local/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1196, in resolve_all
STDERR: 2021-08-11T05:18:30.866816081Z strict_foreign_properties=strict_foreign_properties,
STDERR: 2021-08-11T05:18:30.866818962Z File "/usr/local/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1422, in validate_links
STDERR: 2021-08-11T05:18:30.866822038Z raise errors[0]
STDERR: 2021-08-11T05:18:30.866825246Z schema_salad.exceptions.ValidationException: brats-dream-challenge-infra-main/validation-phase-workflow.cwl:32:1: checking field `steps`
STDERR: 2021-08-11T05:18:30.866829090Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:175:3: checking object
STDERR: 2021-08-11T05:18:30.866832532Z `brats-dream-challenge-infra-main/validation-phase-workflow.cwl#check_final_status`
STDERR: 2021-08-11T05:18:30.866836128Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:177:5: checking field `in`
STDERR: 2021-08-11T05:18:30.866839013Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:178:9: checking object
STDERR: 2021-08-11T05:18:30.866842153Z `brats-dream-challenge-infra-main/validation-phase-workflow.cwl#check_final_status/status`
STDERR: 2021-08-11T05:18:30.866845923Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:179:9: Field `source`
STDERR: 2021-08-11T05:18:30.866849966Z references unknown identifier
STDERR: 2021-08-11T05:18:30.866853720Z `file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#score/status`,
STDERR: 2021-08-11T05:18:30.866858620Z tried
STDERR: 2021-08-11T05:18:30.866861857Z file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#score/status
STDERR: 2021-08-11T05:18:30.866883172Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:182:9: checking object
STDERR: 2021-08-11T05:18:30.866886777Z `brats-dream-challenge-infra-main/validation-phase-workflow.cwl#check_final_status/previous_email_finished`
STDERR: 2021-08-11T05:18:30.866890208Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:183:9: Field `source`
STDERR: 2021-08-11T05:18:30.866893226Z references unknown identifier
STDERR: 2021-08-11T05:18:30.866896421Z `file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#email_score/finished`,
STDERR: 2021-08-11T05:18:30.866899821Z tried
STDERR: 2021-08-11T05:18:30.866903498Z file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f410ff5e-ae85-4a0e-a315-b28207da1e97/brats-dream-challenge-infra-main/validation-phase-workflow.cwl#email_score/finished
Created by Alxaline @Alxaline ,
I don't currently see an error within those logs. To best help, can you let me know what the submission ID is? @vchung new error
STDERR: 2021-08-11T11:16:38.906848943Z 58ab0e4110b2 2021-08-11 11:16:38,906 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-11T11:16:42.860824239Z 58ab0e4110b2 2021-08-11 11:16:42,860 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2021-08-11T11:16:42.860850940Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-11T11:16:42.860854817Z ["null", "File"] may be
STDERR: 2021-08-11T11:16:42.860858616Z incompatible
STDERR: 2021-08-11T11:16:42.860862201Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:135:9: with sink 'input_file' of
STDERR: 2021-08-11T11:16:42.860865525Z type "File"
STDERR: 2021-08-11T11:16:42.860868769Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-11T11:16:42.860871736Z ["null", "File"] may be
STDERR: 2021-08-11T11:16:42.860875057Z incompatible
STDERR: 2021-08-11T11:16:42.860878373Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:75:9: with sink 'input_file' of
STDERR: 2021-08-11T11:16:42.860881482Z type "File"
STDERR: 2021-08-11T11:16:44.190444470Z 58ab0e4110b2 2021-08-11 11:16:44,190 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-11T11:16:44.972124239Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/node-71170403-34a1-496c-9935-bbac84574993-16349ee66b573b0d6cff3dbc6912349f/tmp0p7qx4rj/worker_log.txt
STDERR: 2021-08-11T11:16:45.317237216Z 58ab0e4110b2 2021-08-11 11:16:45,316 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2021-08-11T11:16:45.318542930Z 58ab0e4110b2 2021-08-11 11:16:45,318 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_set_permissions.cwl/instance-14kloo1w with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T11:16:45.318749864Z 58ab0e4110b2 2021-08-11 11:16:45,318 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-g_zv_tdb with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T11:16:45.318969368Z 58ab0e4110b2 2021-08-11 11:16:45,318 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_get_submission.cwl/instance-ds9yiold with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T11:16:46.426970785Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/node-71170403-34a1-496c-9935-bbac84574993-16349ee66b573b0d6cff3dbc6912349f/tmpyi1zl5ck/worker_log.txt
STDERR: 2021-08-11T11:16:46.447776562Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/node-71170403-34a1-496c-9935-bbac84574993-16349ee66b573b0d6cff3dbc6912349f/tmpf2zirrx4/worker_log.txt
STDERR: 2021-08-11T11:16:46.448352398Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/f1418a8c-4f9b-4ee1-81c4-9cf82865aa32/node-71170403-34a1-496c-9935-bbac84574993-16349ee66b573b0d6cff3dbc6912349f/tmpp2f8q46i/worker_log.txt Hi @Alxaline ,
Thank you for participating! A fellow participant has already alerted us of this error and it has been fixed. Your submission has been reset for queue evaluation.