Dear BraTS organizers,
I can see that, for inpainting tasks, the output of the docker should be structured like:
/
├── output
│ ├── BraTS-GLI-00001-100-t1n-inference.nii.gz
│ ├── BraTS-GLI-00002-000-t1n-inference.nii.gz
│ ├── BraTS-GLI-00002-100-t1n-inference.nii.gz
Does this same structure apply to **task 8** , missing MRI synthesis?
Best regards,
Omar Carpentiero
Created by OMAR CARPENTIERO ocarpentiero Hi @bheeshmsharma1 ,
Please submit your Docker models to the **Docker** queues, not validation queues. Hi @branhongweili,
We have made the Docker submission; could you please confirm once?
I am getting this logs:
STDERR: 2025-08-05T12:45:15.483389825Z 0dc59ff06b93 2025-08-05 12:45:15,483 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl'
STDERR: 2025-08-05T12:45:17.903464338Z 0dc59ff06b93 2025-08-05 12:45:17,903 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2025-08-05T12:45:17.903495640Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:87:9: Source 'filepath' of type
STDERR: 2025-08-05T12:45:17.903500751Z ["null", "File"] may be
STDERR: 2025-08-05T12:45:17.903505151Z incompatible
STDERR: 2025-08-05T12:45:17.903509252Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:133:9: with sink 'input_file'
STDERR: 2025-08-05T12:45:17.903513342Z of type "File"
STDERR: 2025-08-05T12:45:17.903517352Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:75:9: Source 'config' of type
STDERR: 2025-08-05T12:45:17.903521492Z ["null", "string"] may be
STDERR: 2025-08-05T12:45:17.903525662Z incompatible
STDERR: 2025-08-05T12:45:17.903529393Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:122:9: with sink 'synapseid' of
STDERR: 2025-08-05T12:45:17.903533323Z type "string"
STDERR: 2025-08-05T12:45:17.903537363Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:87:9: Source 'filepath' of type
STDERR: 2025-08-05T12:45:17.903541414Z ["null", "File"] may be
STDERR: 2025-08-05T12:45:17.903545514Z incompatible
STDERR: 2025-08-05T12:45:17.903549424Z brats-infra-main/wf-segmentation/panoptica-validation-phase.cwl:217:9: with sink 'input_file'
STDERR: 2025-08-05T12:45:17.903553394Z of type "File"
STDERR: 2025-08-05T12:45:18.075022095Z 0dc59ff06b93 2025-08-05 12:45:18,074 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T12:45:18.497158067Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpmi393rej/worker_log.txt
STDERR: 2025-08-05T12:45:18.666630948Z 0dc59ff06b93 2025-08-05 12:45:18,666 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2025-08-05T12:45:18.668462686Z 0dc59ff06b93 2025-08-05 12:45:18,668 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-ebozndkv with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:18.668516269Z 0dc59ff06b93 2025-08-05 12:45:18,668 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-uungeciz with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:18.668600975Z 0dc59ff06b93 2025-08-05 12:45:18,668 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-qh4aoa1u with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:19.099240753Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpk725gqcd/worker_log.txt
STDERR: 2025-08-05T12:45:19.099269565Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpxeo4vi6g/worker_log.txt
STDERR: 2025-08-05T12:45:19.105649536Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpsoaloh3t/worker_log.txt
STDERR: 2025-08-05T12:45:21.488231257Z 0dc59ff06b93 2025-08-05 12:45:21,487 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-qh4aoa1u
STDERR: 2025-08-05T12:45:21.488955294Z 0dc59ff06b93 2025-08-05 12:45:21,488 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-6x2wllbc with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:21.905324084Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpe8dyvdi4/worker_log.txt
STDERR: 2025-08-05T12:45:22.048323851Z 0dc59ff06b93 2025-08-05 12:45:22,047 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-ebozndkv
STDERR: 2025-08-05T12:45:22.078733119Z 0dc59ff06b93 2025-08-05 12:45:22,078 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-6x2wllbc
STDERR: 2025-08-05T12:45:22.079508359Z 0dc59ff06b93 2025-08-05 12:45:22,079 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-a1epgf67 with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:22.079596855Z 0dc59ff06b93 2025-08-05 12:45:22,079 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-009fj2qb with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:22.079705912Z 0dc59ff06b93 2025-08-05 12:45:22,079 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-t73zeeds with job batch system ID: 7 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:22.253661862Z 0dc59ff06b93 2025-08-05 12:45:22,253 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-uungeciz
STDERR: 2025-08-05T12:45:22.521935777Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmppkvf59t5/worker_log.txt
STDERR: 2025-08-05T12:45:22.558809200Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmp6z3wx7r3/worker_log.txt
STDERR: 2025-08-05T12:45:22.565548555Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpkr5s21uz/worker_log.txt
STDERR: 2025-08-05T12:45:24.850252044Z 0dc59ff06b93 2025-08-05 12:45:24,849 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-a1epgf67
STDERR: 2025-08-05T12:45:24.991696731Z 0dc59ff06b93 2025-08-05 12:45:24,991 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-009fj2qb
STDERR: 2025-08-05T12:45:25.183489720Z 0dc59ff06b93 2025-08-05 12:45:25,183 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-t73zeeds
STDERR: 2025-08-05T12:45:25.184190885Z 0dc59ff06b93 2025-08-05 12:45:25,183 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 with job batch system ID: 8 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2025-08-05T12:45:25.599074539Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/node-752e22b6-4e1f-43c1-8b3b-5b7cbb62d52b-1cc402dd0e11d5ae18db04a6de87223d/tmpfcdnxxpp/worker_log.txt
STDERR: 2025-08-05T12:45:25.684592935Z 0dc59ff06b93 2025-08-05 12:45:25,684 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2
STDERR: 2025-08-05T12:45:25.685011672Z 0dc59ff06b93 2025-08-05 12:45:25,684 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2
STDERR: 2025-08-05T12:45:25.685098198Z 0dc59ff06b93 2025-08-05 12:45:25,684 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 follows:
STDERR: 2025-08-05T12:45:25.685104858Z =========>
STDERR: 2025-08-05T12:45:25.685108748Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-05T12:45:25.685112248Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T12:45:25.685115399Z Traceback (most recent call last):
STDERR: 2025-08-05T12:45:25.685118209Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T12:45:25.685121319Z raise WorkflowException(
STDERR: 2025-08-05T12:45:25.685124259Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-05T12:45:25.685127229Z
STDERR: 2025-08-05T12:45:25.685129970Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-05T12:45:25.685132860Z
STDERR: 2025-08-05T12:45:25.685135600Z Traceback (most recent call last):
STDERR: 2025-08-05T12:45:25.685138440Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-05T12:45:25.685141430Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-05T12:45:25.685144291Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-05T12:45:25.685154461Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-05T12:45:25.685157571Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-05T12:45:25.685160492Z return self.run(fileStore)
STDERR: 2025-08-05T12:45:25.685163232Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-05T12:45:25.685166112Z fill_in_defaults(
STDERR: 2025-08-05T12:45:25.685168822Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T12:45:25.685171762Z raise WorkflowException(
STDERR: 2025-08-05T12:45:25.685174483Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-05T12:45:25.685177403Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-05T12:45:25.685180313Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-05T12:45:25.685183293Z ERROR:toil.worker:Exiting the worker because of a failed job on host 0dc59ff06b93
STDERR: 2025-08-05T12:45:25.685187463Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 to 0
STDERR: 2025-08-05T12:45:25.685191274Z <=========
STDERR: 2025-08-05T12:45:25.685883198Z 0dc59ff06b93 2025-08-05 12:45:25,685 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 is completely failed
STDERR: 2025-08-05T12:45:37.125573842Z 0dc59ff06b93 2025-08-05 12:45:37,125 MainThread INFO toil.leader: Finished toil run with 7 failed jobs.
STDERR: 2025-08-05T12:45:37.125651057Z 0dc59ff06b93 2025-08-05 12:45:37,125 MainThread INFO toil.leader: Failed jobs at end of the run: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-6x2wllbc 'CWLWorkflow' kind-CWLWorkflow/instance-7gxvkp2o '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-t73zeeds '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-qh4aoa1u 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 '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-a1epgf67 '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-009fj2qb
STDERR: 2025-08-05T12:45:37.137017847Z Traceback (most recent call last):
STDERR: 2025-08-05T12:45:37.137031408Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2025-08-05T12:45:37.137036049Z sys.exit(main())
STDERR: 2025-08-05T12:45:37.137039299Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2025-08-05T12:45:37.137042659Z outobj = toil.start(wf1)
STDERR: 2025-08-05T12:45:37.137046729Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 829, in start
STDERR: 2025-08-05T12:45:37.137049820Z return self._runMainLoop(rootJobGraph)
STDERR: 2025-08-05T12:45:37.137052650Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 1115, in _runMainLoop
STDERR: 2025-08-05T12:45:37.137055630Z return Leader(config=self.config,
STDERR: 2025-08-05T12:45:37.137058440Z File "/usr/local/lib/python3.8/site-packages/toil/leader.py", line 269, in run
STDERR: 2025-08-05T12:45:37.137061330Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2025-08-05T12:45:37.137065010Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/tmpkvgh7rsw' contains 7 failed jobs: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/get_task.cwl' kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_get_task.cwl/instance-6x2wllbc, 'CWLWorkflow' kind-CWLWorkflow/instance-7gxvkp2o, '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-t73zeeds, '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-qh4aoa1u, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2, '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-a1epgf67, '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-009fj2qb
STDERR: 2025-08-05T12:45:37.137083442Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 follows:
STDERR: 2025-08-05T12:45:37.137087312Z =========>
STDERR: 2025-08-05T12:45:37.137090292Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2025-08-05T12:45:37.137093352Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2025-08-05T12:45:37.137096343Z Traceback (most recent call last):
STDERR: 2025-08-05T12:45:37.137099283Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T12:45:37.137102403Z raise WorkflowException(
STDERR: 2025-08-05T12:45:37.137105243Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2025-08-05T12:45:37.137108183Z
STDERR: 2025-08-05T12:45:37.137110973Z The above exception was the direct cause of the following exception:
STDERR: 2025-08-05T12:45:37.137113914Z
STDERR: 2025-08-05T12:45:37.137116604Z Traceback (most recent call last):
STDERR: 2025-08-05T12:45:37.137119504Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2025-08-05T12:45:37.137122454Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2025-08-05T12:45:37.137125374Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2025-08-05T12:45:37.137128255Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2025-08-05T12:45:37.137131105Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2025-08-05T12:45:37.137134015Z return self.run(fileStore)
STDERR: 2025-08-05T12:45:37.137136795Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2025-08-05T12:45:37.137139715Z fill_in_defaults(
STDERR: 2025-08-05T12:45:37.137143056Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2025-08-05T12:45:37.137146126Z raise WorkflowException(
STDERR: 2025-08-05T12:45:37.137148936Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2025-08-05T12:45:37.137151926Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2025-08-05T12:45:37.137158236Z cwltool.errors.WorkflowException: brats-infra-main/wf-segmentation/steps/validate.cwl:10:3: Missing required input parameter 'input_file'
STDERR: 2025-08-05T12:45:37.137161377Z ERROR:toil.worker:Exiting the worker because of a failed job on host 0dc59ff06b93
STDERR: 2025-08-05T12:45:37.137164467Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/8e04ef26-0890-4bde-87e4-2d1bb92fa602/brats-infra-main/wf-segmentation/steps/validate.cwl' validate2024.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_8e04ef26-0890-4bde-87e4-2d1bb92fa602_brats-infra-main_wf-segmentation_steps_validate.cwl/instance-gm7gtve2 to 0
STDERR: 2025-08-05T12:45:37.137168327Z <=========
Thanks. hi Omar @ocarpentiero,
No, for Task 8, the output format should match the input — there's no need to add "-inference" to the filenames.
Best,
Bran