Hi,
I've successfully tested my Dockerized models on my local system, and it works. However, I received the following error message when I submitted my Dockerized container.
Did you all try to run this container and get this error? On the Docker submission tutorial, it says that the containers will not be run until after the submission timeline ends.
Best,
aec8
```
STDERR: 2025-08-01T12:11:00.328051415Z 50e69b19927f 2025-08-01 12:11:00,327 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/validation-phase.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/validation-phase.cwl'
STDERR: 2025-08-01T12:11:02.703661839Z 50e69b19927f 2025-08-01 12:11:02,703 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2025-08-01T12:11:02.703690000Z brats-infra-main/wf-segmentation/validation-phase.cwl:67:9: Source 'filepath' of type ["null",
STDERR: 2025-08-01T12:11:02.703694650Z "File"] may be incompatible
STDERR: 2025-08-01T12:11:02.703698050Z brats-infra-main/wf-segmentation/validation-phase.cwl:194:9: with sink 'input_file' of type
STDERR: 2025-08-01T12:11:02.703701020Z "File"
STDERR: 2025-08-01T12:11:02.703704020Z brats-infra-main/wf-segmentation/validation-phase.cwl:67:9: Source 'filepath' of type ["null",
STDERR: 2025-08-01T12:11:02.703707040Z "File"] may be incompatible
STDERR: 2025-08-01T12:11:02.703709941Z brats-infra-main/wf-segmentation/validation-phase.cwl:112:9: with sink 'input_file' of type
STDERR: 2025-08-01T12:11:02.703712801Z "File"
STDERR: 2025-08-01T12:11:02.883720769Z 50e69b19927f 2025-08-01 12:11:02,883 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-01T12:11:03.321327168Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmplcz32v0v/worker_log.txt
STDERR: 2025-08-01T12:11:03.485683013Z 50e69b19927f 2025-08-01 12:11:03,485 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2025-08-01T12:11:03.486676307Z 50e69b19927f 2025-08-01 12:11:03,486 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-ruwe3pjg with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:03.486776720Z 50e69b19927f 2025-08-01 12:11:03,486 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-468v2kwh with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:03.904012482Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmprcbikqe7/worker_log.txt
STDERR: 2025-08-01T12:11:03.918812205Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmpb6gfytht/worker_log.txt
STDERR: 2025-08-01T12:11:05.970869954Z 50e69b19927f 2025-08-01 12:11:05,970 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-ruwe3pjg
STDERR: 2025-08-01T12:11:05.971210712Z 50e69b19927f 2025-08-01 12:11:05,971 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-56gg7idi with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:06.350691213Z 50e69b19927f 2025-08-01 12:11:06,350 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-468v2kwh
STDERR: 2025-08-01T12:11:06.422425696Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmpuuclawuk/worker_log.txt
STDERR: 2025-08-01T12:11:06.613153590Z 50e69b19927f 2025-08-01 12:11:06,612 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-56gg7idi
STDERR: 2025-08-01T12:11:06.613656932Z 50e69b19927f 2025-08-01 12:11:06,613 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-4tshdba5 with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:06.613765615Z 50e69b19927f 2025-08-01 12:11:06,613 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-1rauk7cy with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:07.052806209Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmpbst2kber/worker_log.txt
STDERR: 2025-08-01T12:11:07.053015714Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmpnvg55zgq/worker_log.txt
STDERR: 2025-08-01T12:11:09.310165400Z 50e69b19927f 2025-08-01 12:11:09,309 MainThread INFO toil.leader: Job ended: '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-1rauk7cy
STDERR: 2025-08-01T12:11:09.451488464Z 50e69b19927f 2025-08-01 12:11:09,451 MainThread INFO toil.leader: Job ended: '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-4tshdba5
STDERR: 2025-08-01T12:11:09.451939075Z 50e69b19927f 2025-08-01 12:11:09,451 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-01T12:11:09.878276416Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/node-1fae200f-1d35-4401-80e1-23ba428bd5ad-1cc402dd0e11d5ae18db04a6de87223d/tmpjx6dr68z/worker_log.txt
STDERR: 2025-08-01T12:11:09.992566453Z 50e69b19927f 2025-08-01 12:11:09,992 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl
STDERR: 2025-08-01T12:11:09.992871591Z 50e69b19927f 2025-08-01 12:11:09,992 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl
STDERR: 2025-08-01T12:11:09.993008724Z 50e69b19927f 2025-08-01 12:11:09,992 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl follows:
STDERR: 2025-08-01T12:11:09.993015064Z =========>
STDERR: 2025-08-01T12:11:09.993019204Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-01T12:11:09.993022504Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-01T12:11:09.993025834Z Traceback (most recent call last):
STDERR: 2025-08-01T12:11:09.993028984Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-01T12:11:09.993032374Z raise WorkflowException(
STDERR: 2025-08-01T12:11:09.993035484Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-01T12:11:09.993038784Z
STDERR: 2025-08-01T12:11:09.993041795Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-01T12:11:09.993044955Z
STDERR: 2025-08-01T12:11:09.993050785Z Traceback (most recent call last):
STDERR: 2025-08-01T12:11:09.993064195Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-01T12:11:09.993067625Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-01T12:11:09.993070835Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-01T12:11:09.993074125Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-01T12:11:09.993077225Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-01T12:11:09.993080516Z return self.run(fileStore)
STDERR: 2025-08-01T12:11:09.993083536Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-01T12:11:09.993086785Z fill_in_defaults(
STDERR: 2025-08-01T12:11:09.993089986Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-01T12:11:09.993093266Z raise WorkflowException(
STDERR: 2025-08-01T12:11:09.993096256Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-01T12:11:09.993099586Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-01T12:11:09.993102706Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-01T12:11:09.993106056Z ERROR:toil.worker:Exiting the worker because of a failed job on host 50e69b19927f
STDERR: 2025-08-01T12:11:09.993110456Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl to 0
STDERR: 2025-08-01T12:11:09.993115076Z <=========
STDERR: 2025-08-01T12:11:09.993778592Z 50e69b19927f 2025-08-01 12:11:09,993 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl is completely failed
STDERR: 2025-08-01T12:11:21.930360137Z 50e69b19927f 2025-08-01 12:11:21,930 MainThread INFO toil.leader: Finished toil run with 6 failed jobs.
STDERR: 2025-08-01T12:11:21.930391177Z 50e69b19927f 2025-08-01 12:11:21,930 MainThread INFO toil.leader: Failed jobs at end of the run: '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-4tshdba5 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-ruwe3pjg 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-56gg7idi 'CWLWorkflow' kind-CWLWorkflow/instance-dsct1xhu 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl '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-1rauk7cy
STDERR: 2025-08-01T12:11:21.944375362Z Traceback (most recent call last):
STDERR: 2025-08-01T12:11:21.944391733Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2025-08-01T12:11:21.944396643Z sys.exit(main())
STDERR: 2025-08-01T12:11:21.944400113Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2025-08-01T12:11:21.944403473Z outobj = toil.start(wf1)
STDERR: 2025-08-01T12:11:21.944406563Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 829, in start
STDERR: 2025-08-01T12:11:21.944409873Z return self._runMainLoop(rootJobGraph)
STDERR: 2025-08-01T12:11:21.944413043Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 1115, in _runMainLoop
STDERR: 2025-08-01T12:11:21.944416333Z return Leader(config=self.config,
STDERR: 2025-08-01T12:11:21.944419493Z File "/usr/local/lib/python3.8/site-packages/toil/leader.py", line 269, in run
STDERR: 2025-08-01T12:11:21.944422803Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2025-08-01T12:11:21.944427354Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/tmp8exn2tu1' contains 6 failed jobs: '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-4tshdba5, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-ruwe3pjg, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-56gg7idi, 'CWLWorkflow' kind-CWLWorkflow/instance-dsct1xhu, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl, '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-1rauk7cy
STDERR: 2025-08-01T12:11:21.944442334Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl follows:
STDERR: 2025-08-01T12:11:21.944446694Z =========>
STDERR: 2025-08-01T12:11:21.944449874Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-01T12:11:21.944453114Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-01T12:11:21.944456314Z Traceback (most recent call last):
STDERR: 2025-08-01T12:11:21.944459594Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-01T12:11:21.944462924Z raise WorkflowException(
STDERR: 2025-08-01T12:11:21.944466035Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-01T12:11:21.944469304Z
STDERR: 2025-08-01T12:11:21.944472305Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-01T12:11:21.944475495Z
STDERR: 2025-08-01T12:11:21.944478505Z Traceback (most recent call last):
STDERR: 2025-08-01T12:11:21.944481685Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-01T12:11:21.944485025Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-01T12:11:21.944488265Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-01T12:11:21.944491545Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-01T12:11:21.944494705Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-01T12:11:21.944497975Z return self.run(fileStore)
STDERR: 2025-08-01T12:11:21.944501025Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-01T12:11:21.944504285Z fill_in_defaults(
STDERR: 2025-08-01T12:11:21.944507345Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-01T12:11:21.944510705Z raise WorkflowException(
STDERR: 2025-08-01T12:11:21.944513766Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-01T12:11:21.944517096Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-01T12:11:21.944520756Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-01T12:11:21.944527786Z ERROR:toil.worker:Exiting the worker because of a failed job on host 50e69b19927f
STDERR: 2025-08-01T12:11:21.944531216Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/7eb858b5-df73-4eee-a09f-1ecef823dd29/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_7eb858b5-df73-4eee-a09f-1ecef823dd29_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-kvesggbl to 0
STDERR: 2025-08-01T12:11:21.944535886Z <=========
```
Created by aec8 Hi @pjsjongsung ,
Good find! Howevever, the test datasets all use dashes (-) as the delimiter , e.g.
```
/input/
├── BraTS-xxx-xxxxx-xxx
│ ├── BraTS-xxx-xxxxx-xxx-mask.nii.gz
│ └── BraTS-xxx-xxxxx-xxx-t1n-voided.nii.gz
├── BraTS-xxx-yyyyy-yyy
│ ├── BraTS-xxx-yyyyy-yyy-mask.nii.gz
│ └── BraTS-xxx-yyyyy-yyy-t1n-voided.nii.gz
...
``` @vchung I just saw that the MEN sample dataset had its name as subjname_t1c.nii.gz instead of subjname-t1c.nii.gz (according to the wiki it should be a bar not an underbar) could this be the reason? Should we make the code compensate for both cases? @vchung Strange. I guess that means the test is failing after running some of the sample data? (So running ok with GLI but fails and gives no output for MEN) Because we do not enforce any file name other than using the subject's identification number from the sub directory of input.
@CALADAN Thank you for the suggestion, but not that I know of. @vchung Thank you
---
@pjsjongsung is it possible you may have copied your sample data for testing into the docker image? Experienced a simple issue once. @CALADAN ,
Yes, the organizers are performing sanity checks of all submitted containers so that participants have the opportunity to fix their models before the final deadline. If you did not receive a message, it is likely your model(s) were successful on the sample datasets.
---
@pjsjongsung ,
You are correct: only the voided t1 and mask are provided. But let's say you are given MEN voided t1 and masks - the output of your model remains to be the GLI ones. @vchung Thanks for the response!
I must be misunderstanding something. So on the inpainting task, we don't always get a voided t1 and a mask like the validation set? Why would the docker be passed a folder of MEN cases? Hi @vchung .. Thanks for all your hard work.
Does this previous message imply we will receive notification on whether or not our docker submission succeeds checks? Hi @pjsjongsung,
Sorry for not providing a clearer explanation! The issue is that even when different input data is mounted - for example, a folder of MEN cases - the container doesn't generate predictions for that new dataset. The output consistently remains the predictions for the sample dataset. Hello, we got an email that says this:
We received your Docker submission for the BraTS-Lighthouse 2025 Challenge - Task 9. Unfortunately, we are not able to produce predictions for the sample datasets we are mounting. The output of your Docker submission is always the same:
predictions/
├── BraTS-GLI-00000-000-t1n-inference.nii.gz
├── BraTS-GLI-00002-000-t1n-inference.nii.gz
├── BraTS-GLI-00033-000-t1n-inference.nii.gz
└── BraTS-GLI-00072-001-t1n-inference.nii.gz
We don't understand what the issue might be because the file names looks correct. Could anyone help us pinpoint the issue? @vchung
Thank you! Dear,
We've submitted our short paper (paper number 57). when trying to upload docker to our project we get access denied. we created a new project and pushed the docker successfully but when submitting to the challenge we don't have the option "BraTS 2025 - Task 5: BraTS-Africa (Docker)". Can you help us with this?
new project id is: syn68579357
Thanks
@vchung
@CALADAN ,
Thanks for the confirmation. It sounds like you're doing everything correctly! Sorry that you're still experiencing issues.
Although you can't push your image directly to Synapse, you can still add it as an external image, which will allow you to submit it through Synapse still. A workaround for this is provided on the [Submission Tutorial](https://www.synapse.org/Synapse:syn64153130/wiki/633742) under the **"Upload" Your Docker Model** section. Hi @vchung, Thanks for getting back to me.
Yes, I am using MFA and a PAT with modification enabled. Even created a new PAT for reassurance, yet still. Hi @CALADAN ,
Thank you for sharing some context. When logging into the Synapse Docker registry, are you using a Personal Access Token (PAT) with "Modify" permissions enabled? Now that Synapse has required Multi-Factor Authentication (MFA), logging into the registry with a username + password will no longer allow you to push up Docker images.
Let us know,
EDIT: fix wording Hello there,
I'm having a hard time pushing my docker to synapse.
```
docker login docker.synapse.org -u CALADAN
docker push docker.synapse.org/syn68233053/dock:v1
denied: requested access to the resource is denied
```
It was working fine a day ago, and now I get 'denied'.
I own the project, and I'm a certified user.
@the_heavy_shadow,
Congrats on getting to the finish line!
> What is next? Should I just wait for the results?
Yes, the Challenge Organizers will begin running all submitted containers on Aug 8th against the unseen test data and will announce the results at a later time. Thank you @vchung! It feels good that I got to the end line.
What is next? Should I just wait for the results? @the_heavy_shadow ,
Your submission was received and the logfile you shared seems normal. You're good! @CMENGYNN ,
Please submit your Docker model to the _Docker_ queues, not validation queues. ###Docker Submission Errors
Hello, HELP!!
I've successfully tested my Docker on my local host, and it works. However, I received the following error message when I submitted my Dockerized container.
The prompt I input is like:
_docker run \
--rm \
--network none \
--gpus=all \
--volume /mnt/s/glioma_nnunet/Analyze_Results/docker_submission/input:/input:ro \
--volume /mnt/s/glioma_nnunet/Analyze_Results/docker_submission/output:/output:rw \
--memory=16G --shm-size 4G \
docker.synapse.org/syn68610899/brats_peds_submission:v1_
in terminal UBUNTU-22.04, and the progress successfully work, and save the segment mask in my assigned output folder.
However, I received the following error message when I submitted my Dockerized container in to the challenge system. It shows the following **ERROR!!!!!!** from Submission Dashboard (submission ID: 9756475)
Best,
CMENGYNN
STDERR: 2025-08-05T06:03:50.661330841Z 790fac8e49b5 2025-08-05 06:03:50,661 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/validation-phase.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/validation-phase.cwl'
STDERR: 2025-08-05T06:03:52.932161670Z 790fac8e49b5 2025-08-05 06:03:52,931 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2025-08-05T06:03:52.932189720Z brats-infra-main/wf-segmentation/validation-phase.cwl:67:9: Source 'filepath' of type ["null",
STDERR: 2025-08-05T06:03:52.932194231Z "File"] may be incompatible
STDERR: 2025-08-05T06:03:52.932197611Z brats-infra-main/wf-segmentation/validation-phase.cwl:194:9: with sink 'input_file' of type
STDERR: 2025-08-05T06:03:52.932200501Z "File"
STDERR: 2025-08-05T06:03:52.932203331Z brats-infra-main/wf-segmentation/validation-phase.cwl:67:9: Source 'filepath' of type ["null",
STDERR: 2025-08-05T06:03:52.932206291Z "File"] may be incompatible
STDERR: 2025-08-05T06:03:52.932209131Z brats-infra-main/wf-segmentation/validation-phase.cwl:112:9: with sink 'input_file' of type
STDERR: 2025-08-05T06:03:52.932211961Z "File"
STDERR: 2025-08-05T06:03:53.104715976Z 790fac8e49b5 2025-08-05 06:03:53,104 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T06:03:53.545581371Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmp9_q9mnyg/worker_log.txt
STDERR: 2025-08-05T06:03:53.706298346Z 790fac8e49b5 2025-08-05 06:03:53,706 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2025-08-05T06:03:53.707277785Z 790fac8e49b5 2025-08-05 06:03:53,707 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-579xv4nt with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:53.707346657Z 790fac8e49b5 2025-08-05 06:03:53,707 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-a6m3d8cj with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:54.133135303Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmpoj78ka2a/worker_log.txt
STDERR: 2025-08-05T06:03:54.137295789Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmptyuz0tn3/worker_log.txt
STDERR: 2025-08-05T06:03:56.309986236Z 790fac8e49b5 2025-08-05 06:03:56,309 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-579xv4nt
STDERR: 2025-08-05T06:03:56.310446495Z 790fac8e49b5 2025-08-05 06:03:56,310 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-gqayjlhp with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:56.659006019Z 790fac8e49b5 2025-08-05 06:03:56,658 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-a6m3d8cj
STDERR: 2025-08-05T06:03:56.741014800Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmphf0f6_da/worker_log.txt
STDERR: 2025-08-05T06:03:56.901367506Z 790fac8e49b5 2025-08-05 06:03:56,900 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-gqayjlhp
STDERR: 2025-08-05T06:03:56.901681262Z 790fac8e49b5 2025-08-05 06:03:56,901 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-582ffv1t with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:56.901790134Z 790fac8e49b5 2025-08-05 06:03:56,901 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-jaz9ppwi with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:57.324191102Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmpwd51s7o7/worker_log.txt
STDERR: 2025-08-05T06:03:57.327274205Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmp9x9ohsf7/worker_log.txt
STDERR: 2025-08-05T06:03:59.354989936Z 790fac8e49b5 2025-08-05 06:03:59,354 MainThread INFO toil.leader: Job ended: '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-jaz9ppwi
STDERR: 2025-08-05T06:03:59.486360309Z 790fac8e49b5 2025-08-05 06:03:59,486 MainThread INFO toil.leader: Job ended: '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-582ffv1t
STDERR: 2025-08-05T06:03:59.486850730Z 790fac8e49b5 2025-08-05 06:03:59,486 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T06:03:59.909775384Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/node-3e02996a-d0e6-40d4-bfb8-1a3206249692-1cc402dd0e11d5ae18db04a6de87223d/tmpbwt53lbl/worker_log.txt
STDERR: 2025-08-05T06:03:59.997041921Z 790fac8e49b5 2025-08-05 06:03:59,996 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v
STDERR: 2025-08-05T06:03:59.997445910Z 790fac8e49b5 2025-08-05 06:03:59,997 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v
STDERR: 2025-08-05T06:03:59.997578593Z 790fac8e49b5 2025-08-05 06:03:59,997 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v follows:
STDERR: 2025-08-05T06:03:59.997588774Z =========>
STDERR: 2025-08-05T06:03:59.997593044Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-05T06:03:59.997596304Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T06:03:59.997599374Z Traceback (most recent call last):
STDERR: 2025-08-05T06:03:59.997602134Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T06:03:59.997605144Z raise WorkflowException(
STDERR: 2025-08-05T06:03:59.997607904Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-05T06:03:59.997610694Z
STDERR: 2025-08-05T06:03:59.997613514Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-05T06:03:59.997616314Z
STDERR: 2025-08-05T06:03:59.997618954Z Traceback (most recent call last):
STDERR: 2025-08-05T06:03:59.997633305Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-05T06:03:59.997638765Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-05T06:03:59.997643975Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-05T06:03:59.997649075Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-05T06:03:59.997653745Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-05T06:03:59.997658445Z return self.run(fileStore)
STDERR: 2025-08-05T06:03:59.997662825Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-05T06:03:59.997666925Z fill_in_defaults(
STDERR: 2025-08-05T06:03:59.997669706Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T06:03:59.997672626Z raise WorkflowException(
STDERR: 2025-08-05T06:03:59.997675306Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-05T06:03:59.997678146Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-05T06:03:59.997680966Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-05T06:03:59.997683836Z ERROR:toil.worker:Exiting the worker because of a failed job on host 790fac8e49b5
STDERR: 2025-08-05T06:03:59.997692106Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v to 0
STDERR: 2025-08-05T06:03:59.997696126Z <=========
STDERR: 2025-08-05T06:03:59.998306750Z 790fac8e49b5 2025-08-05 06:03:59,998 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v is completely failed
STDERR: 2025-08-05T06:04:11.150703072Z 790fac8e49b5 2025-08-05 06:04:11,150 MainThread INFO toil.leader: Finished toil run with 6 failed jobs.
STDERR: 2025-08-05T06:04:11.150726772Z 790fac8e49b5 2025-08-05 06:04:11,150 MainThread INFO toil.leader: Failed jobs at end of the run: '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-582ffv1t 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-579xv4nt '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-jaz9ppwi 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-gqayjlhp 'CWLWorkflow' kind-CWLWorkflow/instance-btaq60bv
STDERR: 2025-08-05T06:04:11.164169188Z Traceback (most recent call last):
STDERR: 2025-08-05T06:04:11.164182639Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2025-08-05T06:04:11.164186939Z sys.exit(main())
STDERR: 2025-08-05T06:04:11.164190029Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2025-08-05T06:04:11.164193329Z outobj = toil.start(wf1)
STDERR: 2025-08-05T06:04:11.164196079Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 829, in start
STDERR: 2025-08-05T06:04:11.164198909Z return self._runMainLoop(rootJobGraph)
STDERR: 2025-08-05T06:04:11.164201669Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 1115, in _runMainLoop
STDERR: 2025-08-05T06:04:11.164204489Z return Leader(config=self.config,
STDERR: 2025-08-05T06:04:11.164207229Z File "/usr/local/lib/python3.8/site-packages/toil/leader.py", line 269, in run
STDERR: 2025-08-05T06:04:11.164210179Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2025-08-05T06:04:11.164214360Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/tmpdv325390' contains 6 failed jobs: '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-582ffv1t, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-579xv4nt, '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-jaz9ppwi, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-gqayjlhp, 'CWLWorkflow' kind-CWLWorkflow/instance-btaq60bv
STDERR: 2025-08-05T06:04:11.164226090Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v follows:
STDERR: 2025-08-05T06:04:11.164232220Z =========>
STDERR: 2025-08-05T06:04:11.164237280Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-05T06:04:11.164242010Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T06:04:11.164246840Z Traceback (most recent call last):
STDERR: 2025-08-05T06:04:11.164251320Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T06:04:11.164256260Z raise WorkflowException(
STDERR: 2025-08-05T06:04:11.164261000Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-05T06:04:11.164265870Z
STDERR: 2025-08-05T06:04:11.164268701Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-05T06:04:11.164271501Z
STDERR: 2025-08-05T06:04:11.164274231Z Traceback (most recent call last):
STDERR: 2025-08-05T06:04:11.164276961Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-05T06:04:11.164279801Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-05T06:04:11.164282651Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-05T06:04:11.164285461Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-05T06:04:11.164288161Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-05T06:04:11.164290951Z return self.run(fileStore)
STDERR: 2025-08-05T06:04:11.164293621Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-05T06:04:11.164296451Z fill_in_defaults(
STDERR: 2025-08-05T06:04:11.164299161Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T06:04:11.164302031Z raise WorkflowException(
STDERR: 2025-08-05T06:04:11.164304741Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-05T06:04:11.164307621Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-05T06:04:11.164310731Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-05T06:04:11.164317711Z ERROR:toil.worker:Exiting the worker because of a failed job on host 790fac8e49b5
STDERR: 2025-08-05T06:04:11.164320762Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/c480f2a6-1a24-480d-aeee-a257413b3811/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_c480f2a6-1a24-480d-aeee-a257413b3811_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-avrewk6v to 0
STDERR: 2025-08-05T06:04:11.164325182Z <=========
Best,
CMENGYNN @astaraki Could you please help?
Hi,
I can run my docker image, and the container successfully generates the outputs. However, my submission was not successful. Here is the log:
STDERR: 2025-08-04T03:08:33.629403704Z ddd626db82df 2025-08-04 03:08:33,628 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/docker-validation.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/docker-validation.cwl'
STDERR: 2025-08-04T03:08:36.208690618Z ddd626db82df 2025-08-04 03:08:36,208 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-04T03:08:37.072514696Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmpjmgmq888/worker_log.txt
STDERR: 2025-08-04T03:08:37.300289212Z ddd626db82df 2025-08-04 03:08:37,299 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2025-08-04T03:08:37.300921535Z ddd626db82df 2025-08-04 03:08:37,300 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/check_submission_type.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_check_submission_type.cwl/instance-ymbswcpq with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:38.103744465Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmpq25nqtly/worker_log.txt
STDERR: 2025-08-04T03:08:40.586355661Z ddd626db82df 2025-08-04 03:08:40,585 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/check_submission_type.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_check_submission_type.cwl/instance-ymbswcpq
STDERR: 2025-08-04T03:08:40.587268261Z ddd626db82df 2025-08-04 03:08:40,587 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-bwkwp2z3 with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:40.587516796Z ddd626db82df 2025-08-04 03:08:40,587 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/email_results.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_email_results.cwl/instance-ucgqj1ap with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:41.400148005Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmp73tejt5z/worker_log.txt
STDERR: 2025-08-04T03:08:41.411674120Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmp7moidkyn/worker_log.txt
STDERR: 2025-08-04T03:08:44.776899134Z ddd626db82df 2025-08-04 03:08:44,776 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-bwkwp2z3
STDERR: 2025-08-04T03:08:45.308846841Z ddd626db82df 2025-08-04 03:08:45,308 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/email_results.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_email_results.cwl/instance-ucgqj1ap
STDERR: 2025-08-04T03:08:45.309388033Z ddd626db82df 2025-08-04 03:08:45,309 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_check_status.cwl/instance-c45xk3ds with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:46.133546557Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmpqptlp05l/worker_log.txt
STDERR: 2025-08-04T03:08:46.454099656Z ddd626db82df 2025-08-04 03:08:46,453 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_check_status.cwl/instance-c45xk3ds
STDERR: 2025-08-04T03:08:46.454594147Z ddd626db82df 2025-08-04 03:08:46,454 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-bwkwp2z3 with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:46.454887183Z ddd626db82df 2025-08-04 03:08:46,454 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/email_results.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_email_results.cwl/instance-ucgqj1ap with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:47.274524621Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmp3ffh7p04/worker_log.txt
STDERR: 2025-08-04T03:08:47.297651874Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmp04crmiv4/worker_log.txt
STDERR: 2025-08-04T03:08:47.439667545Z ddd626db82df 2025-08-04 03:08:47,439 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-bwkwp2z3
STDERR: 2025-08-04T03:08:47.470184873Z ddd626db82df 2025-08-04 03:08:47,469 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/email_results.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_email_results.cwl/instance-ucgqj1ap
STDERR: 2025-08-04T03:08:47.470616853Z ddd626db82df 2025-08-04 03:08:47,470 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/check_submission_type.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_check_submission_type.cwl/instance-ymbswcpq with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2025-08-04T03:08:48.271929761Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmp7k_md9z9/worker_log.txt
STDERR: 2025-08-04T03:08:48.412017231Z ddd626db82df 2025-08-04 03:08:48,411 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/brats-infra-main/wf-containers/steps/check_submission_type.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_6795bc1e-3833-40c3-9742-8297fab7410c_brats-infra-main_wf-containers_steps_check_submission_type.cwl/instance-ymbswcpq
STDERR: 2025-08-04T03:08:49.211639762Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmpr3bvd46o/worker_log.txt
STDERR: 2025-08-04T03:08:50.176455019Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/node-c5bfceb4-43dd-4280-8ddd-a3eecf96fa93-1cc402dd0e11d5ae18db04a6de87223d/tmpp3sepopm/worker_log.txt
STDERR: 2025-08-04T03:08:52.272638123Z ddd626db82df 2025-08-04 03:08:52,272 MainThread INFO toil.leader: Finished toil run successfully.
STDERR: 2025-08-04T03:08:52.292138087Z ddd626db82df 2025-08-04 03:08:52,291 MainThread INFO toil.common: Successfully deleted the job store: FileJobStore(/var/lib/docker/volumes/workflow_orchestrator_shared/_data/6795bc1e-3833-40c3-9742-8297fab7410c/tmp_8pl94jo)
STDOUT: 2025-08-04T03:08:52.566671330Z {}
I should highlight that without "--shm-size=8g \", my container fails locally. This is how I run my docker image:
docker run --rm --gpus all \
--shm-size=8g \
-v [LocalPath]/data:/input:ro \
-v [LocalPath]/inference:/output \
[ImageName] /bin/bash Hi @aec8,
You are correct - we are not running your Docker containers at this time.
Based on the logs, you may have submitted your Docker model to one of the validation queues instead, which is expecting file submissions (hence the error about the missing `input_file`).
Hope this helps!