Hi, Log file looks there was something critically wrong . The submitted result was generated by the same way, which we used in previous BraTS(2018,2019,2020). Any idea or advice would be appreciated! Cheers STDERR: 2021-08-03T13:31:04.533131862Z 058861c5becc 2021-08-03 13:31:04,532 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' STDERR: 2021-08-03T13:31:08.314509867Z 058861c5becc 2021-08-03 13:31:08,314 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2021-08-03T13:31:08.314555951Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-03T13:31:08.314560743Z ["null", "File"] may be STDERR: 2021-08-03T13:31:08.314564496Z incompatible STDERR: 2021-08-03T13:31:08.314567953Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:62:9: with sink 'input_file' of STDERR: 2021-08-03T13:31:08.314571339Z type "File" STDERR: 2021-08-03T13:31:08.314574683Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-03T13:31:08.314577936Z ["null", "File"] may be STDERR: 2021-08-03T13:31:08.314581284Z incompatible STDERR: 2021-08-03T13:31:08.314584538Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:122:9: with sink 'input_file' of STDERR: 2021-08-03T13:31:08.314588174Z type "File" STDERR: 2021-08-03T13:31:09.585672359Z 058861c5becc 2021-08-03 13:31:09,585 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T13:31:10.346006571Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpoqi7j1jn/worker_log.txt STDERR: 2021-08-03T13:31:10.620598891Z 058861c5becc 2021-08-03 13:31:10,620 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2021-08-03T13:31:10.621370677Z 058861c5becc 2021-08-03 13:31:10,621 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-ctutatzt with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:10.621588365Z 058861c5becc 2021-08-03 13:31:10,621 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-27pv9uyu with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:11.717106338Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpq7iq294l/worker_log.txt STDERR: 2021-08-03T13:31:11.756701416Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpx8mws9zi/worker_log.txt STDERR: 2021-08-03T13:31:14.974802345Z 058861c5becc 2021-08-03 13:31:14,973 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-27pv9uyu STDERR: 2021-08-03T13:31:15.024285334Z 058861c5becc 2021-08-03 13:31:15,024 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-ctutatzt STDERR: 2021-08-03T13:31:15.025057445Z 058861c5becc 2021-08-03 13:31:15,024 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_validate.cwl/instance-lxbsg_62 with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:15.988877179Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmp29rennd5/worker_log.txt STDERR: 2021-08-03T13:31:17.787059134Z 058861c5becc 2021-08-03 13:31:17,786 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_validate.cwl/instance-lxbsg_62 STDERR: 2021-08-03T13:31:17.788149592Z 058861c5becc 2021-08-03 13:31:17,787 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-bgi5t54n with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:17.788435838Z 058861c5becc 2021-08-03 13:31:17,788 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-f59vl2mi with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:18.928133598Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpktr5s9od/worker_log.txt STDERR: 2021-08-03T13:31:18.928178185Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmp4qizd8uk/worker_log.txt STDERR: 2021-08-03T13:31:21.897952643Z 058861c5becc 2021-08-03 13:31:21,897 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-bgi5t54n STDERR: 2021-08-03T13:31:21.989994831Z 058861c5becc 2021-08-03 13:31:21,989 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-f59vl2mi STDERR: 2021-08-03T13:31:21.990637744Z 058861c5becc 2021-08-03 13:31:21,990 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-hzkpuakm with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:22.699421210Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmprq513zvj/worker_log.txt STDERR: 2021-08-03T13:31:22.959928637Z 058861c5becc 2021-08-03 13:31:22,959 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-hzkpuakm STDERR: 2021-08-03T13:31:22.960638476Z 058861c5becc 2021-08-03 13:31:22,960 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-03T13:31:23.677547292Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/worker_log.txt STDERR: 2021-08-03T13:31:41.239619465Z 058861c5becc 2021-08-03 13:31:41,237 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg STDERR: 2021-08-03T13:31:41.240479810Z 058861c5becc 2021-08-03 13:31:41,240 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg STDERR: 2021-08-03T13:31:41.240921922Z 058861c5becc 2021-08-03 13:31:41,240 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg follows: STDERR: 2021-08-03T13:31:41.240944461Z =========> STDERR: 2021-08-03T13:31:41.240948864Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-03T13:31:41.240952131Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T13:31:41.240955663Z [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: 2021-08-03T13:31:41.240975560Z 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: 2021-08-03T13:31:41.240980057Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q$ docker \ STDERR: 2021-08-03T13:31:41.240983728Z run \ STDERR: 2021-08-03T13:31:41.240986799Z -i \ STDERR: 2021-08-03T13:31:41.240989713Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q,target=/DZMlbA \ STDERR: 2021-08-03T13:31:41.240993234Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwvhog8h4j,target=/tmp \ STDERR: 2021-08-03T13:31:41.240997687Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpleemgv3w.tmp,target=/var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig,readonly \ STDERR: 2021-08-03T13:31:41.241001404Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpcn3i0v8y.tmp,target=/var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060,readonly \ STDERR: 2021-08-03T13:31:41.241005018Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpst0z8ytw.tmp,target=/var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T13:31:41.241009260Z --workdir=/DZMlbA \ STDERR: 2021-08-03T13:31:41.241108358Z --read-only=true \ STDERR: 2021-08-03T13:31:41.241112838Z --user=0:0 \ STDERR: 2021-08-03T13:31:41.241116236Z --rm \ STDERR: 2021-08-03T13:31:41.241119553Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T13:31:41.241128318Z --env=HOME=/DZMlbA \ STDERR: 2021-08-03T13:31:41.241131930Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwbzewgnv0/20210803133123-754064.cid \ STDERR: 2021-08-03T13:31:41.241136266Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T13:31:41.241139673Z score.py \ STDERR: 2021-08-03T13:31:41.241142770Z --parent_id \ STDERR: 2021-08-03T13:31:41.241145873Z syn26025536 \ STDERR: 2021-08-03T13:31:41.241151538Z -s \ STDERR: 2021-08-03T13:31:41.241154485Z /var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig \ STDERR: 2021-08-03T13:31:41.241157818Z -p \ STDERR: 2021-08-03T13:31:41.241160707Z /var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060 \ STDERR: 2021-08-03T13:31:41.241163920Z -g \ STDERR: 2021-08-03T13:31:41.241167177Z /var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T13:31:41.241183737Z -c \ STDERR: 2021-08-03T13:31:41.241186985Z /work/CaPTk \ STDERR: 2021-08-03T13:31:41.241190120Z -o \ STDERR: 2021-08-03T13:31:41.241192389Z results.json STDERR: 2021-08-03T13:31:41.241194645Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q$ docker \ STDERR: 2021-08-03T13:31:41.241197475Z run \ STDERR: 2021-08-03T13:31:41.241199790Z -i \ STDERR: 2021-08-03T13:31:41.241203329Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q,target=/DZMlbA \ STDERR: 2021-08-03T13:31:41.241206126Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwvhog8h4j,target=/tmp \ STDERR: 2021-08-03T13:31:41.241208805Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpleemgv3w.tmp,target=/var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig,readonly \ STDERR: 2021-08-03T13:31:41.241211601Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpcn3i0v8y.tmp,target=/var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060,readonly \ STDERR: 2021-08-03T13:31:41.241217526Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpst0z8ytw.tmp,target=/var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T13:31:41.241220334Z --workdir=/DZMlbA \ STDERR: 2021-08-03T13:31:41.241222584Z --read-only=true \ STDERR: 2021-08-03T13:31:41.241224704Z --user=0:0 \ STDERR: 2021-08-03T13:31:41.241226930Z --rm \ STDERR: 2021-08-03T13:31:41.241229722Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T13:31:41.241231822Z --env=HOME=/DZMlbA \ STDERR: 2021-08-03T13:31:41.241234058Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwbzewgnv0/20210803133123-754064.cid \ STDERR: 2021-08-03T13:31:41.241236666Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T13:31:41.241239139Z score.py \ STDERR: 2021-08-03T13:31:41.241241354Z --parent_id \ STDERR: 2021-08-03T13:31:41.241244507Z syn26025536 \ STDERR: 2021-08-03T13:31:41.241246794Z -s \ STDERR: 2021-08-03T13:31:41.241259818Z /var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig \ STDERR: 2021-08-03T13:31:41.241263308Z -p \ STDERR: 2021-08-03T13:31:41.241266320Z /var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060 \ STDERR: 2021-08-03T13:31:41.241269891Z -g \ STDERR: 2021-08-03T13:31:41.241273077Z /var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T13:31:41.241276694Z -c \ STDERR: 2021-08-03T13:31:41.241279055Z /work/CaPTk \ STDERR: 2021-08-03T13:31:41.241281286Z -o \ STDERR: 2021-08-03T13:31:41.241283355Z results.json STDERR: 2021-08-03T13:31:41.241285479Z [21] Failed to execute script Hausdorff95 STDERR: 2021-08-03T13:31:41.241287677Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:41.241289942Z File "Hausdorff95.py", line 34, in STDERR: 2021-08-03T13:31:41.241292377Z File "site-packages/medpy/metric/binary.py", line 396, in hd95 STDERR: 2021-08-03T13:31:41.241294708Z File "site-packages/medpy/metric/binary.py", line 1224, in __surface_distances STDERR: 2021-08-03T13:31:41.241297029Z File "site-packages/scipy/ndimage/morphology.py", line 2201, in distance_transform_edt STDERR: 2021-08-03T13:31:41.241299349Z MemoryError: Unable to allocate 102. MiB for an array with shape (3, 155, 240, 240) and data type int32 STDERR: 2021-08-03T13:31:41.241301614Z terminate called after throwing an instance of 'std::out_of_range' STDERR: 2021-08-03T13:31:41.241303893Z what(): basic_string::erase: __pos (which is 18446744073709551615) > this->size() (which is 0) STDERR: 2021-08-03T13:31:41.241309145Z /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: 2021-08-03T13:31:41.241311775Z warnings.warn(msg) STDERR: 2021-08-03T13:31:41.241313878Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:41.241316149Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-03T13:31:41.241318482Z main() STDERR: 2021-08-03T13:31:41.241320685Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-03T13:31:41.241322962Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-03T13:31:41.241325134Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-03T13:31:41.241327395Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-03T13:31:41.241329555Z File "/usr/local/bin/score.py", line 63, in run_captk STDERR: 2021-08-03T13:31:41.241332366Z subprocess.check_call(cmd) STDERR: 2021-08-03T13:31:41.241335613Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-03T13:31:41.241339010Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-03T13:31:41.241342251Z 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']' died with . STDERR: 2021-08-03T13:31:41.241346562Z [job score.cwl] Max memory used: 848MiB STDERR: 2021-08-03T13:31:41.241350684Z INFO:cwltool:[job score.cwl] Max memory used: 848MiB STDERR: 2021-08-03T13:31:41.241354005Z [job score.cwl] Job error: STDERR: 2021-08-03T13:31:41.241356794Z ("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: 2021-08-03T13:31:41.241359426Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-03T13:31:41.241361705Z ("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: 2021-08-03T13:31:41.241364310Z [job score.cwl] completed permanentFail STDERR: 2021-08-03T13:31:41.241366475Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-03T13:31:41.241368715Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:41.241370859Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-03T13:31:41.241373179Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-03T13:31:41.241375425Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-03T13:31:41.241377676Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-03T13:31:41.241382316Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-03T13:31:41.241384645Z return self.run(fileStore) STDERR: 2021-08-03T13:31:41.241386811Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-03T13:31:41.241389100Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-03T13:31:41.241391272Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-03T13:31:41.241393439Z ERROR:toil.worker:Exiting the worker because of a failed job on host 058861c5becc STDERR: 2021-08-03T13:31:41.241395853Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg to 0 STDERR: 2021-08-03T13:31:41.241399147Z <========= STDERR: 2021-08-03T13:31:41.242424804Z 058861c5becc 2021-08-03 13:31:41,242 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg is completely failed STDERR: 2021-08-03T13:31:54.693306538Z 058861c5becc 2021-08-03 13:31:54,692 MainThread INFO toil.leader: Finished toil run with 8 failed jobs. STDERR: 2021-08-03T13:31:54.693449191Z 058861c5becc 2021-08-03 13:31:54,693 MainThread INFO toil.leader: Failed jobs at end of the run: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg '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-bgi5t54n '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-ctutatzt '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-f59vl2mi 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_validate.cwl/instance-lxbsg_62 '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-hzkpuakm 'CWLWorkflow' kind-CWLWorkflow/instance-fen69m6q '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-27pv9uyu STDERR: 2021-08-03T13:31:54.743021795Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:54.743052015Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2021-08-03T13:31:54.743056081Z sys.exit(main()) STDERR: 2021-08-03T13:31:54.743058613Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2021-08-03T13:31:54.743061209Z outobj = toil.start(wf1) STDERR: 2021-08-03T13:31:54.743063552Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start STDERR: 2021-08-03T13:31:54.743065944Z return self._runMainLoop(rootJobGraph) STDERR: 2021-08-03T13:31:54.743068243Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop STDERR: 2021-08-03T13:31:54.743070549Z jobCache=self._jobCache).run() STDERR: 2021-08-03T13:31:54.743073218Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run STDERR: 2021-08-03T13:31:54.743076585Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2021-08-03T13:31:54.743112224Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/tmphyc1bnts' contains 8 failed jobs: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg, '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-bgi5t54n, '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-ctutatzt, '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-f59vl2mi, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_validate.cwl/instance-lxbsg_62, '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-hzkpuakm, 'CWLWorkflow' kind-CWLWorkflow/instance-fen69m6q, '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-27pv9uyu STDERR: 2021-08-03T13:31:54.743130562Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_5e4b2156-aa0e-4e84-a3cb-5fb36933a803_brats-dream-challenge-infra-main_score.cwl/instance-eb9apxlg follows: STDERR: 2021-08-03T13:31:54.743133903Z =========> STDERR: 2021-08-03T13:31:54.743136103Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-03T13:31:54.743138332Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-03T13:31:54.743140621Z [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: 2021-08-03T13:31:54.743143147Z 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: 2021-08-03T13:31:54.743146525Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q$ docker \ STDERR: 2021-08-03T13:31:54.743177788Z run \ STDERR: 2021-08-03T13:31:54.743180102Z -i \ STDERR: 2021-08-03T13:31:54.743182816Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q,target=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743186359Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwvhog8h4j,target=/tmp \ STDERR: 2021-08-03T13:31:54.743190217Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpleemgv3w.tmp,target=/var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig,readonly \ STDERR: 2021-08-03T13:31:54.743194082Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpcn3i0v8y.tmp,target=/var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060,readonly \ STDERR: 2021-08-03T13:31:54.743282185Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpst0z8ytw.tmp,target=/var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T13:31:54.743292189Z --workdir=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743295405Z --read-only=true \ STDERR: 2021-08-03T13:31:54.743298496Z --user=0:0 \ STDERR: 2021-08-03T13:31:54.743301261Z --rm \ STDERR: 2021-08-03T13:31:54.743303440Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T13:31:54.743305725Z --env=HOME=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743308571Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwbzewgnv0/20210803133123-754064.cid \ STDERR: 2021-08-03T13:31:54.743311450Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T13:31:54.743313619Z score.py \ STDERR: 2021-08-03T13:31:54.743315814Z --parent_id \ STDERR: 2021-08-03T13:31:54.743317891Z syn26025536 \ STDERR: 2021-08-03T13:31:54.743320070Z -s \ STDERR: 2021-08-03T13:31:54.743322223Z /var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig \ STDERR: 2021-08-03T13:31:54.743324461Z -p \ STDERR: 2021-08-03T13:31:54.743326535Z /var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060 \ STDERR: 2021-08-03T13:31:54.743328816Z -g \ STDERR: 2021-08-03T13:31:54.743330934Z /var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T13:31:54.743333235Z -c \ STDERR: 2021-08-03T13:31:54.743335305Z /work/CaPTk \ STDERR: 2021-08-03T13:31:54.743337384Z -o \ STDERR: 2021-08-03T13:31:54.743339459Z results.json STDERR: 2021-08-03T13:31:54.743341621Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q$ docker \ STDERR: 2021-08-03T13:31:54.743344188Z run \ STDERR: 2021-08-03T13:31:54.743346277Z -i \ STDERR: 2021-08-03T13:31:54.743348387Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/thmhmueor/tmp-outnhx3ur8q,target=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743350986Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwvhog8h4j,target=/tmp \ STDERR: 2021-08-03T13:31:54.743353816Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpleemgv3w.tmp,target=/var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig,readonly \ STDERR: 2021-08-03T13:31:54.743360804Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpcn3i0v8y.tmp,target=/var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060,readonly \ STDERR: 2021-08-03T13:31:54.743365736Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/tmpst0z8ytw.tmp,target=/var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-03T13:31:54.743369803Z --workdir=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743373010Z --read-only=true \ STDERR: 2021-08-03T13:31:54.743376088Z --user=0:0 \ STDERR: 2021-08-03T13:31:54.743379530Z --rm \ STDERR: 2021-08-03T13:31:54.743381785Z --env=TMPDIR=/tmp \ STDERR: 2021-08-03T13:31:54.743383869Z --env=HOME=/DZMlbA \ STDERR: 2021-08-03T13:31:54.743386009Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/5e4b2156-aa0e-4e84-a3cb-5fb36933a803/node-5e9cee5c-3404-4409-ba16-af8270b18b6a-16349ee66b573b0d6cff3dbc6912349f/tmpl85llmvo/81377920-2f58-4616-aa66-9d4d9126fef6/t0y_p44zwbzewgnv0/20210803133123-754064.cid \ STDERR: 2021-08-03T13:31:54.743388652Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-03T13:31:54.743391130Z score.py \ STDERR: 2021-08-03T13:31:54.743393310Z --parent_id \ STDERR: 2021-08-03T13:31:54.743395571Z syn26025536 \ STDERR: 2021-08-03T13:31:54.743397610Z -s \ STDERR: 2021-08-03T13:31:54.743399818Z /var/lib/cwl/stg0e39ab6f-c15f-4eb2-9648-3993e0d9e4f2/.synapseConfig \ STDERR: 2021-08-03T13:31:54.743402047Z -p \ STDERR: 2021-08-03T13:31:54.743404222Z /var/lib/cwl/stgfbed752c-ef87-4722-a509-9a0fa45e4488/submission-9713060 \ STDERR: 2021-08-03T13:31:54.743406416Z -g \ STDERR: 2021-08-03T13:31:54.743408597Z /var/lib/cwl/stg665ea41d-5469-40ff-83af-b0b1a8a9db5a/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-03T13:31:54.743410817Z -c \ STDERR: 2021-08-03T13:31:54.743412845Z /work/CaPTk \ STDERR: 2021-08-03T13:31:54.743414930Z -o \ STDERR: 2021-08-03T13:31:54.743416982Z results.json STDERR: 2021-08-03T13:31:54.743419058Z [21] Failed to execute script Hausdorff95 STDERR: 2021-08-03T13:31:54.743421207Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:54.743423343Z File "Hausdorff95.py", line 34, in STDERR: 2021-08-03T13:31:54.743425762Z File "site-packages/medpy/metric/binary.py", line 396, in hd95 STDERR: 2021-08-03T13:31:54.743428083Z File "site-packages/medpy/metric/binary.py", line 1224, in __surface_distances STDERR: 2021-08-03T13:31:54.743430400Z File "site-packages/scipy/ndimage/morphology.py", line 2201, in distance_transform_edt STDERR: 2021-08-03T13:31:54.743435383Z MemoryError: Unable to allocate 102. MiB for an array with shape (3, 155, 240, 240) and data type int32 STDERR: 2021-08-03T13:31:54.743438881Z terminate called after throwing an instance of 'std::out_of_range' STDERR: 2021-08-03T13:31:54.743442016Z what(): basic_string::erase: __pos (which is 18446744073709551615) > this->size() (which is 0) STDERR: 2021-08-03T13:31:54.743446287Z /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: 2021-08-03T13:31:54.743449880Z warnings.warn(msg) STDERR: 2021-08-03T13:31:54.743453007Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:54.743455947Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-03T13:31:54.743458399Z main() STDERR: 2021-08-03T13:31:54.743460567Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-03T13:31:54.743462863Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-03T13:31:54.743464989Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-03T13:31:54.743467180Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-03T13:31:54.743469278Z File "/usr/local/bin/score.py", line 63, in run_captk STDERR: 2021-08-03T13:31:54.743471490Z subprocess.check_call(cmd) STDERR: 2021-08-03T13:31:54.743473591Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-03T13:31:54.743475867Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-03T13:31:54.743478016Z 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']' died with . STDERR: 2021-08-03T13:31:54.743480671Z [job score.cwl] Max memory used: 848MiB STDERR: 2021-08-03T13:31:54.743482767Z INFO:cwltool:[job score.cwl] Max memory used: 848MiB STDERR: 2021-08-03T13:31:54.743484924Z [job score.cwl] Job error: STDERR: 2021-08-03T13:31:54.743487037Z ("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: 2021-08-03T13:31:54.743489612Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-03T13:31:54.743491777Z ("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: 2021-08-03T13:31:54.743494299Z [job score.cwl] completed permanentFail STDERR: 2021-08-03T13:31:54.743496387Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-03T13:31:54.743498519Z Traceback (most recent call last): STDERR: 2021-08-03T13:31:54.743500654Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-03T13:31:54.743505271Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-03T13:31:54.743507582Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-03T13:31:54.743509860Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-03T13:31:54.743512026Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-03T13:31:54.743514894Z return self.run(fileStore) STDERR: 2021-08-03T13:31:54.743518012Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run