Hi Team, Could you please help me out here? My failure log content is: STDERR: 2021-08-03T12:36:08.119055004Z 360bcb88c87e 2021-08-03 12:36:08,118 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' STDERR: 2021-08-03T12:36:11.616045267Z 360bcb88c87e 2021-08-03 12:36:11,615 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2021-08-03T12:36:11.616080733Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-03T12:36:11.616085123Z ["null", "File"] may be STDERR: 2021-08-03T12:36:11.616089051Z incompatible STDERR: 2021-08-03T12:36:11.616092494Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:122:9: with sink 'input_file' of STDERR: 2021-08-03T12:36:11.616096469Z type "File" STDERR: 2021-08-03T12:36:11.616099900Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-03T12:36:11.616103608Z ["null", "File"] may be STDERR: 2021-08-03T12:36:11.616107340Z incompatible STDERR: 2021-08-03T12:36:11.616110529Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:62:9: with sink 'input_file' of STDERR: 2021-08-03T12:36:11.616113882Z type "File" STDERR: 2021-08-03T12:36:12.883161215Z 360bcb88c87e 2021-08-03 12:36:12,882 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T12:36:13.775831547Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmpe2rsnhse/worker_log.txt STDERR: 2021-08-03T12:36:14.110428655Z 360bcb88c87e 2021-08-03 12:36:14,110 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2021-08-03T12:36:14.111213814Z 360bcb88c87e 2021-08-03 12:36:14,111 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-rbq3ecf2 with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:14.111390609Z 360bcb88c87e 2021-08-03 12:36:14,111 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-olhn5n0j with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:15.258653970Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp9xikz_tt/worker_log.txt STDERR: 2021-08-03T12:36:15.258708806Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp5pdsubal/worker_log.txt STDERR: 2021-08-03T12:36:18.635590805Z 360bcb88c87e 2021-08-03 12:36:18,633 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-olhn5n0j STDERR: 2021-08-03T12:36:19.453182274Z 360bcb88c87e 2021-08-03 12:36:19,452 MainThread INFO toil.leader: Job ended: '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-rbq3ecf2 STDERR: 2021-08-03T12:36:19.454052006Z 360bcb88c87e 2021-08-03 12:36:19,453 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_validate.cwl/instance-mhdiqhac with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:20.207088865Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmpnut45mxx/worker_log.txt STDERR: 2021-08-03T12:36:22.185205510Z 360bcb88c87e 2021-08-03 12:36:22,184 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_validate.cwl/instance-mhdiqhac STDERR: 2021-08-03T12:36:22.186098198Z 360bcb88c87e 2021-08-03 12:36:22,185 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-k4uewe36 with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:22.186282353Z 360bcb88c87e 2021-08-03 12:36:22,186 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-rl0aff2j with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:23.336067224Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmpjp0u3_oz/worker_log.txt STDERR: 2021-08-03T12:36:23.336166793Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmpipbote51/worker_log.txt STDERR: 2021-08-03T12:36:26.377470913Z 360bcb88c87e 2021-08-03 12:36:26,377 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-k4uewe36 STDERR: 2021-08-03T12:36:26.499152252Z 360bcb88c87e 2021-08-03 12:36:26,498 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-rl0aff2j STDERR: 2021-08-03T12:36:26.499778670Z 360bcb88c87e 2021-08-03 12:36:26,499 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-dyl8gdfi with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:27.227403750Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp__c90vxn/worker_log.txt STDERR: 2021-08-03T12:36:27.500547257Z 360bcb88c87e 2021-08-03 12:36:27,500 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-dyl8gdfi STDERR: 2021-08-03T12:36:27.501368917Z 360bcb88c87e 2021-08-03 12:36:27,501 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T12:36:28.218499083Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/worker_log.txt STDERR: 2021-08-03T12:36:31.557739748Z 360bcb88c87e 2021-08-03 12:36:31,557 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef STDERR: 2021-08-03T12:36:31.558333841Z 360bcb88c87e 2021-08-03 12:36:31,558 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef STDERR: 2021-08-03T12:36:31.558729870Z 360bcb88c87e 2021-08-03 12:36:31,558 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef follows: STDERR: 2021-08-03T12:36:31.558753277Z =========> STDERR: 2021-08-03T12:36:31.558775297Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-03T12:36:31.558778797Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T12:36:31.558782452Z [job score.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-03T12:36:31.558786616Z WARNING:cwltool:[job score.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-03T12:36:31.558790509Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_$ docker \ STDERR: 2021-08-03T12:36:31.558794523Z run \ STDERR: 2021-08-03T12:36:31.558797903Z -i \ STDERR: 2021-08-03T12:36:31.558801231Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_,target=/xmTOYm \ STDERR: 2021-08-03T12:36:31.558805133Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r67nuaraof,target=/tmp \ STDERR: 2021-08-03T12:36:31.558810148Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpdv8e6m49.tmp,target=/var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig,readonly \ STDERR: 2021-08-03T12:36:31.558814464Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmphjb0vsr2.tmp,target=/var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051,readonly \ STDERR: 2021-08-03T12:36:31.558818562Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpmy489gwb.tmp,target=/var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T12:36:31.558822342Z --workdir=/xmTOYm \ STDERR: 2021-08-03T12:36:31.558825522Z --read-only=true \ STDERR: 2021-08-03T12:36:31.558828520Z --user=0:0 \ STDERR: 2021-08-03T12:36:31.558831787Z --rm \ STDERR: 2021-08-03T12:36:31.558834811Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T12:36:31.558853521Z --env=HOME=/xmTOYm \ STDERR: 2021-08-03T12:36:31.558857076Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r6acbp8auj/20210803123628-295354.cid \ STDERR: 2021-08-03T12:36:31.558860702Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T12:36:31.558863918Z score.py \ STDERR: 2021-08-03T12:36:31.558867248Z --parent_id \ STDERR: 2021-08-03T12:36:31.558870546Z syn26025435 \ STDERR: 2021-08-03T12:36:31.558874040Z -s \ STDERR: 2021-08-03T12:36:31.558877439Z /var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig \ STDERR: 2021-08-03T12:36:31.558880970Z -p \ STDERR: 2021-08-03T12:36:31.558884039Z /var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051 \ STDERR: 2021-08-03T12:36:31.558887319Z -g \ STDERR: 2021-08-03T12:36:31.558892694Z /var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T12:36:31.558896307Z -c \ STDERR: 2021-08-03T12:36:31.558899316Z /work/CaPTk \ STDERR: 2021-08-03T12:36:31.558902636Z -o \ STDERR: 2021-08-03T12:36:31.558905728Z results.json STDERR: 2021-08-03T12:36:31.558908693Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_$ docker \ STDERR: 2021-08-03T12:36:31.558912321Z run \ STDERR: 2021-08-03T12:36:31.558915439Z -i \ STDERR: 2021-08-03T12:36:31.558966419Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_,target=/xmTOYm \ STDERR: 2021-08-03T12:36:31.558972392Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r67nuaraof,target=/tmp \ STDERR: 2021-08-03T12:36:31.558976005Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpdv8e6m49.tmp,target=/var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig,readonly \ STDERR: 2021-08-03T12:36:31.558980187Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmphjb0vsr2.tmp,target=/var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051,readonly \ STDERR: 2021-08-03T12:36:31.558988509Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpmy489gwb.tmp,target=/var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T12:36:31.558992964Z --workdir=/xmTOYm \ STDERR: 2021-08-03T12:36:31.558995981Z --read-only=true \ STDERR: 2021-08-03T12:36:31.559008342Z --user=0:0 \ STDERR: 2021-08-03T12:36:31.559012538Z --rm \ STDERR: 2021-08-03T12:36:31.559015854Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T12:36:31.559019107Z --env=HOME=/xmTOYm \ STDERR: 2021-08-03T12:36:31.559022226Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r6acbp8auj/20210803123628-295354.cid \ STDERR: 2021-08-03T12:36:31.559026597Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T12:36:31.559029928Z score.py \ STDERR: 2021-08-03T12:36:31.559033349Z --parent_id \ STDERR: 2021-08-03T12:36:31.559036989Z syn26025435 \ STDERR: 2021-08-03T12:36:31.559040421Z -s \ STDERR: 2021-08-03T12:36:31.559043726Z /var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig \ STDERR: 2021-08-03T12:36:31.559047279Z -p \ STDERR: 2021-08-03T12:36:31.559050408Z /var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051 \ STDERR: 2021-08-03T12:36:31.559053956Z -g \ STDERR: 2021-08-03T12:36:31.559057116Z /var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T12:36:31.559069550Z -c \ STDERR: 2021-08-03T12:36:31.559073420Z /work/CaPTk \ STDERR: 2021-08-03T12:36:31.559076678Z -o \ STDERR: 2021-08-03T12:36:31.559080175Z results.json STDERR: 2021-08-03T12:36:31.559083265Z Origin mismatch > 100100%' in axis '1'. STDERR: 2021-08-03T12:36:31.559087658Z Images are not aligned, please ensure both images have the same origin, spacing and direction cosines before trying to extract similarity measures (use '-inf' for image information). STDERR: 2021-08-03T12:36:31.559091303Z Origin for input 1: STDERR: 2021-08-03T12:36:31.559094674Z [0, -239, 0] STDERR: 2021-08-03T12:36:31.559097516Z Origin for input 2: STDERR: 2021-08-03T12:36:31.559100834Z [0, 0, 0] STDERR: 2021-08-03T12:36:31.559104085Z /usr/local/lib/python3.6/site-packages/pandas/compat/__init__.py:120: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. STDERR: 2021-08-03T12:36:31.559108278Z warnings.warn(msg) STDERR: 2021-08-03T12:36:31.559111678Z Traceback (most recent call last): STDERR: 2021-08-03T12:36:31.559118921Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-03T12:36:31.559122591Z main() STDERR: 2021-08-03T12:36:31.559125779Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-03T12:36:31.559129363Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-03T12:36:31.559132826Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-03T12:36:31.559136150Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-03T12:36:31.559139526Z File "/usr/local/bin/score.py", line 63, in run_captk STDERR: 2021-08-03T12:36:31.559142818Z subprocess.check_call(cmd) STDERR: 2021-08-03T12:36:31.559146147Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-03T12:36:31.559149634Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-03T12:36:31.559152877Z subprocess.CalledProcessError: Command '['/work/CaPTk/bin/Utilities', '-i', 'RSNA_ASNR_MICCAI_BraTS2021_ValidationGT/BraTS2021_00001_seg.nii.gz', '-lsb', 'BraTS2021_00001.nii.gz', '-o', 'tmp.csv']' returned non-zero exit status 1. STDERR: 2021-08-03T12:36:31.559156605Z [job score.cwl] Max memory used: 0MiB STDERR: 2021-08-03T12:36:31.559159867Z INFO:cwltool:[job score.cwl] Max memory used: 0MiB STDERR: 2021-08-03T12:36:31.559163237Z [job score.cwl] Job error: STDERR: 2021-08-03T12:36:31.559166343Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/score.cwl:46:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-03T12:36:31.559170199Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-03T12:36:31.559222471Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/score.cwl:46:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-03T12:36:31.559228291Z [job score.cwl] completed permanentFail STDERR: 2021-08-03T12:36:31.559231636Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-03T12:36:31.559235270Z Traceback (most recent call last): STDERR: 2021-08-03T12:36:31.559238457Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-03T12:36:31.559241780Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-03T12:36:31.559244817Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-03T12:36:31.559247910Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-03T12:36:31.559259694Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-03T12:36:31.559264225Z return self.run(fileStore) STDERR: 2021-08-03T12:36:31.559267464Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-03T12:36:31.559271029Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-03T12:36:31.559278349Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-03T12:36:31.559281665Z ERROR:toil.worker:Exiting the worker because of a failed job on host 360bcb88c87e STDERR: 2021-08-03T12:36:31.559284927Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef to 0 STDERR: 2021-08-03T12:36:31.559289927Z <========= STDERR: 2021-08-03T12:36:31.559337812Z 360bcb88c87e 2021-08-03 12:36:31,559 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef is completely failed STDERR: 2021-08-03T12:36:44.953761861Z 360bcb88c87e 2021-08-03 12:36:44,953 MainThread INFO toil.leader: Finished toil run with 8 failed jobs. STDERR: 2021-08-03T12:36:44.954077543Z 360bcb88c87e 2021-08-03 12:36:44,953 MainThread INFO toil.leader: Failed jobs at end of the run: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_validate.cwl/instance-mhdiqhac 'CWLWorkflow' kind-CWLWorkflow/instance-f887osze 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-rl0aff2j 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-k4uewe36 '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-rbq3ecf2 '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-olhn5n0j 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-dyl8gdfi STDERR: 2021-08-03T12:36:44.987148932Z Traceback (most recent call last): STDERR: 2021-08-03T12:36:44.987196086Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2021-08-03T12:36:44.987201422Z sys.exit(main()) STDERR: 2021-08-03T12:36:44.987204714Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2021-08-03T12:36:44.987208228Z outobj = toil.start(wf1) STDERR: 2021-08-03T12:36:44.987211418Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start STDERR: 2021-08-03T12:36:44.987215010Z return self._runMainLoop(rootJobGraph) STDERR: 2021-08-03T12:36:44.987218815Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop STDERR: 2021-08-03T12:36:44.987222372Z jobCache=self._jobCache).run() STDERR: 2021-08-03T12:36:44.987225369Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run STDERR: 2021-08-03T12:36:44.987228834Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2021-08-03T12:36:44.988102997Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/tmp9he8x6d3' contains 8 failed jobs: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_validate.cwl/instance-mhdiqhac, 'CWLWorkflow' kind-CWLWorkflow/instance-f887osze, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-rl0aff2j, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-k4uewe36, '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-rbq3ecf2, '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-olhn5n0j, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-dyl8gdfi STDERR: 2021-08-03T12:36:44.988121203Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef follows: STDERR: 2021-08-03T12:36:44.988125267Z =========> STDERR: 2021-08-03T12:36:44.988138282Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-03T12:36:44.988141915Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T12:36:44.988145611Z [job score.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-03T12:36:44.988149775Z WARNING:cwltool:[job score.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-03T12:36:44.988153715Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_$ docker \ STDERR: 2021-08-03T12:36:44.988157902Z run \ STDERR: 2021-08-03T12:36:44.988161093Z -i \ STDERR: 2021-08-03T12:36:44.988164575Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_,target=/xmTOYm \ STDERR: 2021-08-03T12:36:44.988168365Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r67nuaraof,target=/tmp \ STDERR: 2021-08-03T12:36:44.988172038Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpdv8e6m49.tmp,target=/var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig,readonly \ STDERR: 2021-08-03T12:36:44.988175733Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmphjb0vsr2.tmp,target=/var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051,readonly \ STDERR: 2021-08-03T12:36:44.988179763Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpmy489gwb.tmp,target=/var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T12:36:44.988184208Z --workdir=/xmTOYm \ STDERR: 2021-08-03T12:36:44.988187235Z --read-only=true \ STDERR: 2021-08-03T12:36:44.988190460Z --user=0:0 \ STDERR: 2021-08-03T12:36:44.988193435Z --rm \ STDERR: 2021-08-03T12:36:44.988196678Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T12:36:44.988199711Z --env=HOME=/xmTOYm \ STDERR: 2021-08-03T12:36:44.988955409Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r6acbp8auj/20210803123628-295354.cid \ STDERR: 2021-08-03T12:36:44.988974309Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T12:36:44.989012521Z score.py \ STDERR: 2021-08-03T12:36:44.989016311Z --parent_id \ STDERR: 2021-08-03T12:36:44.989019648Z syn26025435 \ STDERR: 2021-08-03T12:36:44.989022577Z -s \ STDERR: 2021-08-03T12:36:44.989025631Z /var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig \ STDERR: 2021-08-03T12:36:44.989029091Z -p \ STDERR: 2021-08-03T12:36:44.989032548Z /var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051 \ STDERR: 2021-08-03T12:36:44.989036198Z -g \ STDERR: 2021-08-03T12:36:44.989039554Z /var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T12:36:44.989042794Z -c \ STDERR: 2021-08-03T12:36:44.989046082Z /work/CaPTk \ STDERR: 2021-08-03T12:36:44.989049368Z -o \ STDERR: 2021-08-03T12:36:44.989052690Z results.json STDERR: 2021-08-03T12:36:44.989056806Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_$ docker \ STDERR: 2021-08-03T12:36:44.989060866Z run \ STDERR: 2021-08-03T12:36:44.989269878Z -i \ STDERR: 2021-08-03T12:36:44.989275502Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tznkizx0p/tmp-outlnv95vk_,target=/xmTOYm \ STDERR: 2021-08-03T12:36:44.989279635Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r67nuaraof,target=/tmp \ STDERR: 2021-08-03T12:36:44.989283287Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpdv8e6m49.tmp,target=/var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig,readonly \ STDERR: 2021-08-03T12:36:44.989313804Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmphjb0vsr2.tmp,target=/var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051,readonly \ STDERR: 2021-08-03T12:36:44.989318713Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tmpmy489gwb.tmp,target=/var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T12:36:44.989366429Z --workdir=/xmTOYm \ STDERR: 2021-08-03T12:36:44.989370213Z --read-only=true \ STDERR: 2021-08-03T12:36:44.989373377Z --user=0:0 \ STDERR: 2021-08-03T12:36:44.989376443Z --rm \ STDERR: 2021-08-03T12:36:44.989380004Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T12:36:44.989383624Z --env=HOME=/xmTOYm \ STDERR: 2021-08-03T12:36:44.989386598Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/node-e15d8879-7c68-4fe1-b17c-b3d8b9f350ef-16349ee66b573b0d6cff3dbc6912349f/tmp8_v9v61g/283addc3-8bd3-4cf0-93c8-d18a63725c7c/tynrfw2r6acbp8auj/20210803123628-295354.cid \ STDERR: 2021-08-03T12:36:44.989389951Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T12:36:44.989393289Z score.py \ STDERR: 2021-08-03T12:36:44.989396145Z --parent_id \ STDERR: 2021-08-03T12:36:44.989399277Z syn26025435 \ STDERR: 2021-08-03T12:36:44.989402469Z -s \ STDERR: 2021-08-03T12:36:44.989405564Z /var/lib/cwl/stg7f31442f-aa55-4341-855a-863cdf5acb3a/.synapseConfig \ STDERR: 2021-08-03T12:36:44.989439796Z -p \ STDERR: 2021-08-03T12:36:44.989446499Z /var/lib/cwl/stgc4c3bc42-9a74-4b28-b9a4-c75d0c25b867/submission-9713051 \ STDERR: 2021-08-03T12:36:44.989450431Z -g \ STDERR: 2021-08-03T12:36:44.989454160Z /var/lib/cwl/stgd1c8e40b-3143-4100-a206-bfe9e9db3de6/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T12:36:44.989458190Z -c \ STDERR: 2021-08-03T12:36:44.989461498Z /work/CaPTk \ STDERR: 2021-08-03T12:36:44.989464884Z -o \ STDERR: 2021-08-03T12:36:44.989468330Z results.json STDERR: 2021-08-03T12:36:44.989559714Z Origin mismatch > 100100%' in axis '1'. STDERR: 2021-08-03T12:36:44.989566911Z Images are not aligned, please ensure both images have the same origin, spacing and direction cosines before trying to extract similarity measures (use '-inf' for image information). STDERR: 2021-08-03T12:36:44.989570732Z Origin for input 1: STDERR: 2021-08-03T12:36:44.989574836Z [0, -239, 0] STDERR: 2021-08-03T12:36:44.989578261Z Origin for input 2: STDERR: 2021-08-03T12:36:44.989613673Z [0, 0, 0] STDERR: 2021-08-03T12:36:44.989619220Z /usr/local/lib/python3.6/site-packages/pandas/compat/__init__.py:120: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. STDERR: 2021-08-03T12:36:44.989623636Z warnings.warn(msg) STDERR: 2021-08-03T12:36:44.989627108Z Traceback (most recent call last): STDERR: 2021-08-03T12:36:44.989630928Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-03T12:36:44.989640128Z main() STDERR: 2021-08-03T12:36:44.989643412Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-03T12:36:44.989666808Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-03T12:36:44.989670544Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-03T12:36:44.989675585Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-03T12:36:44.989679275Z File "/usr/local/bin/score.py", line 63, in run_captk STDERR: 2021-08-03T12:36:44.989683211Z subprocess.check_call(cmd) STDERR: 2021-08-03T12:36:44.989686961Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-03T12:36:44.989690923Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-03T12:36:44.989694599Z subprocess.CalledProcessError: Command '['/work/CaPTk/bin/Utilities', '-i', 'RSNA_ASNR_MICCAI_BraTS2021_ValidationGT/BraTS2021_00001_seg.nii.gz', '-lsb', 'BraTS2021_00001.nii.gz', '-o', 'tmp.csv']' returned non-zero exit status 1. STDERR: 2021-08-03T12:36:44.989698874Z [job score.cwl] Max memory used: 0MiB STDERR: 2021-08-03T12:36:44.989702564Z INFO:cwltool:[job score.cwl] Max memory used: 0MiB STDERR: 2021-08-03T12:36:44.989706152Z [job score.cwl] Job error: STDERR: 2021-08-03T12:36:44.989709851Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/score.cwl:46:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-03T12:36:44.989714131Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-03T12:36:44.989717500Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/score.cwl:46:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-03T12:36:44.989721864Z [job score.cwl] completed permanentFail STDERR: 2021-08-03T12:36:44.989725278Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-03T12:36:44.989728427Z Traceback (most recent call last): STDERR: 2021-08-03T12:36:44.989731944Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-03T12:36:44.989735584Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-03T12:36:44.989739700Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-03T12:36:44.989743664Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-03T12:36:44.989747732Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-03T12:36:44.989751560Z return self.run(fileStore) STDERR: 2021-08-03T12:36:44.989755494Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-03T12:36:44.989759691Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-03T12:36:44.989763514Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-03T12:36:44.989771591Z ERROR:toil.worker:Exiting the worker because of a failed job on host 360bcb88c87e STDERR: 2021-08-03T12:36:44.989777214Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/d4deba50-b7cf-49cd-8510-4e0774cd1b41/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_d4deba50-b7cf-49cd-8510-4e0774cd1b41_brats-dream-challenge-infra-main_score.cwl/instance-ygp1c6ef to 0 STDERR: 2021-08-03T12:36:44.989782291Z <========= Thanks, Ryanrui