Dear Organizers, We uploaded our results and got this log file. We don't know what we are wrong with. Please help us. Thank you. Best regards, MIP team Log file detail: STDERR: 2021-08-02T12:00:53.870328413Z 053b70656255 2021-08-02 12:00:53,870 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' STDERR: 2021-08-02T12:00:56.858271023Z 053b70656255 2021-08-02 12:00:56,857 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2021-08-02T12:00:56.858301877Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-02T12:00:56.858306208Z ["null", "File"] may be STDERR: 2021-08-02T12:00:56.858309743Z incompatible STDERR: 2021-08-02T12:00:56.858312943Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:62:9: with sink 'input_file' of STDERR: 2021-08-02T12:00:56.858316371Z type "File" STDERR: 2021-08-02T12:00:56.858319803Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-02T12:00:56.858323795Z ["null", "File"] may be STDERR: 2021-08-02T12:00:56.858357489Z incompatible STDERR: 2021-08-02T12:00:56.858360985Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:120:9: with sink 'input_file' of STDERR: 2021-08-02T12:00:56.858364201Z type "File" STDERR: 2021-08-02T12:00:58.269736140Z 053b70656255 2021-08-02 12:00:58,268 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T12:00:59.450040831Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmp9frdt3xm/worker_log.txt STDERR: 2021-08-02T12:00:59.717028341Z 053b70656255 2021-08-02 12:00:59,716 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2021-08-02T12:00:59.717843723Z 053b70656255 2021-08-02 12:00:59,717 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-m5dpdjk4 with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:00:59.717999763Z 053b70656255 2021-08-02 12:00:59,717 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-1qe4usyv with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:00.833580091Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpnqllj2ik/worker_log.txt STDERR: 2021-08-02T12:01:00.868409300Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpto5k3dz8/worker_log.txt STDERR: 2021-08-02T12:01:04.698149089Z 053b70656255 2021-08-02 12:01:04,695 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-1qe4usyv STDERR: 2021-08-02T12:01:05.096024305Z 053b70656255 2021-08-02 12:01:05,095 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-m5dpdjk4 STDERR: 2021-08-02T12:01:05.096712115Z 053b70656255 2021-08-02 12:01:05,096 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_validate.cwl/instance-s_w00veo with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:05.864172130Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpuvh31rc1/worker_log.txt STDERR: 2021-08-02T12:01:07.610359668Z 053b70656255 2021-08-02 12:01:07,610 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_validate.cwl/instance-s_w00veo STDERR: 2021-08-02T12:01:07.611188511Z 053b70656255 2021-08-02 12:01:07,611 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-9jweq38g with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:07.611345806Z 053b70656255 2021-08-02 12:01:07,611 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-c5b7nkhu with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:08.748786667Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmp1o5nll8w/worker_log.txt STDERR: 2021-08-02T12:01:08.755460092Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmp24nw20zk/worker_log.txt STDERR: 2021-08-02T12:01:11.720241100Z 053b70656255 2021-08-02 12:01:11,719 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-c5b7nkhu STDERR: 2021-08-02T12:01:11.841994046Z 053b70656255 2021-08-02 12:01:11,841 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-9jweq38g STDERR: 2021-08-02T12:01:11.842655913Z 053b70656255 2021-08-02 12:01:11,842 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-vfs2ry8i with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:12.553141601Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmp106ec4ck/worker_log.txt STDERR: 2021-08-02T12:01:12.811753304Z 053b70656255 2021-08-02 12:01:12,811 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-vfs2ry8i STDERR: 2021-08-02T12:01:12.812413045Z 053b70656255 2021-08-02 12:01:12,812 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T12:01:13.527633554Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/worker_log.txt STDERR: 2021-08-02T12:01:15.821299968Z 053b70656255 2021-08-02 12:01:15,820 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 STDERR: 2021-08-02T12:01:15.821826207Z 053b70656255 2021-08-02 12:01:15,821 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 STDERR: 2021-08-02T12:01:15.822140327Z 053b70656255 2021-08-02 12:01:15,821 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 follows: STDERR: 2021-08-02T12:01:15.822161292Z =========> STDERR: 2021-08-02T12:01:15.822165246Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-02T12:01:15.822168353Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T12:01:15.822171637Z [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: 2021-08-02T12:01:15.822175333Z 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: 2021-08-02T12:01:15.822179084Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr$ docker \ STDERR: 2021-08-02T12:01:15.822183091Z run \ STDERR: 2021-08-02T12:01:15.822186403Z -i \ STDERR: 2021-08-02T12:01:15.822189654Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr,target=/yKRORp \ STDERR: 2021-08-02T12:01:15.822194092Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x70mtw4_km,target=/tmp \ STDERR: 2021-08-02T12:01:15.822198813Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmp2l104iur.tmp,target=/var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig,readonly \ STDERR: 2021-08-02T12:01:15.822203201Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpn35q_ajc.tmp,target=/var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941,readonly \ STDERR: 2021-08-02T12:01:15.822207237Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpwi07pfbh.tmp,target=/var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T12:01:15.822211613Z --workdir=/yKRORp \ STDERR: 2021-08-02T12:01:15.822214970Z --read-only=true \ STDERR: 2021-08-02T12:01:15.822218328Z --user=0:0 \ STDERR: 2021-08-02T12:01:15.822221537Z --rm \ STDERR: 2021-08-02T12:01:15.822224851Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T12:01:15.822231157Z --env=HOME=/yKRORp \ STDERR: 2021-08-02T12:01:15.822234671Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x7jmukg_x5/20210802120113-604337.cid \ STDERR: 2021-08-02T12:01:15.822238714Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T12:01:15.822241875Z score.py \ STDERR: 2021-08-02T12:01:15.822244954Z --parent_id \ STDERR: 2021-08-02T12:01:15.822248238Z syn26020966 \ STDERR: 2021-08-02T12:01:15.822251456Z -s \ STDERR: 2021-08-02T12:01:15.822254552Z /var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig \ STDERR: 2021-08-02T12:01:15.822258067Z -p \ STDERR: 2021-08-02T12:01:15.822261563Z /var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941 \ STDERR: 2021-08-02T12:01:15.822265110Z -g \ STDERR: 2021-08-02T12:01:15.822268030Z /var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T12:01:15.822271213Z -c \ STDERR: 2021-08-02T12:01:15.822274195Z /work/CaPTk \ STDERR: 2021-08-02T12:01:15.822277135Z -o \ STDERR: 2021-08-02T12:01:15.822280207Z results.json STDERR: 2021-08-02T12:01:15.822283231Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr$ docker \ STDERR: 2021-08-02T12:01:15.822287466Z run \ STDERR: 2021-08-02T12:01:15.822290647Z -i \ STDERR: 2021-08-02T12:01:15.822294090Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr,target=/yKRORp \ STDERR: 2021-08-02T12:01:15.822297841Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x70mtw4_km,target=/tmp \ STDERR: 2021-08-02T12:01:15.822301664Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmp2l104iur.tmp,target=/var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig,readonly \ STDERR: 2021-08-02T12:01:15.822305654Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpn35q_ajc.tmp,target=/var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941,readonly \ STDERR: 2021-08-02T12:01:15.822313012Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpwi07pfbh.tmp,target=/var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T12:01:15.822317839Z --workdir=/yKRORp \ STDERR: 2021-08-02T12:01:15.822321199Z --read-only=true \ STDERR: 2021-08-02T12:01:15.822324550Z --user=0:0 \ STDERR: 2021-08-02T12:01:15.822327770Z --rm \ STDERR: 2021-08-02T12:01:15.822330779Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T12:01:15.822334001Z --env=HOME=/yKRORp \ STDERR: 2021-08-02T12:01:15.822337421Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x7jmukg_x5/20210802120113-604337.cid \ STDERR: 2021-08-02T12:01:15.822341750Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T12:01:15.822345080Z score.py \ STDERR: 2021-08-02T12:01:15.822348126Z --parent_id \ STDERR: 2021-08-02T12:01:15.822351654Z syn26020966 \ STDERR: 2021-08-02T12:01:15.822354867Z -s \ STDERR: 2021-08-02T12:01:15.822358213Z /var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig \ STDERR: 2021-08-02T12:01:15.822361361Z -p \ STDERR: 2021-08-02T12:01:15.822364546Z /var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941 \ STDERR: 2021-08-02T12:01:15.822367832Z -g \ STDERR: 2021-08-02T12:01:15.822371165Z /var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T12:01:15.822374858Z -c \ STDERR: 2021-08-02T12:01:15.822377901Z /work/CaPTk \ STDERR: 2021-08-02T12:01:15.822380928Z -o \ STDERR: 2021-08-02T12:01:15.822384041Z results.json STDERR: 2021-08-02T12:01:15.822387260Z Origin mismatch > 100100%' in axis '1'. STDERR: 2021-08-02T12:01:15.822390587Z 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: 2021-08-02T12:01:15.822394110Z Origin for input 1: STDERR: 2021-08-02T12:01:15.822397098Z [0, -239, 0] STDERR: 2021-08-02T12:01:15.822400188Z Origin for input 2: STDERR: 2021-08-02T12:01:15.822403367Z [0, 0, 0] STDERR: 2021-08-02T12:01:15.822406648Z /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: 2021-08-02T12:01:15.822410631Z warnings.warn(msg) STDERR: 2021-08-02T12:01:15.822413534Z Traceback (most recent call last): STDERR: 2021-08-02T12:01:15.822419908Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-02T12:01:15.822423598Z main() STDERR: 2021-08-02T12:01:15.822426988Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-02T12:01:15.822430653Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-02T12:01:15.822434030Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-02T12:01:15.822437322Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-02T12:01:15.822440600Z File "/usr/local/bin/score.py", line 64, in run_captk STDERR: 2021-08-02T12:01:15.822444247Z subprocess.check_call(cmd) STDERR: 2021-08-02T12:01:15.822447784Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-02T12:01:15.822454274Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-02T12:01:15.822458035Z 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: 2021-08-02T12:01:15.822461862Z [job score.cwl] Max memory used: 0MiB STDERR: 2021-08-02T12:01:15.822465286Z INFO:cwltool:[job score.cwl] Max memory used: 0MiB STDERR: 2021-08-02T12:01:15.822468955Z [job score.cwl] Job error: STDERR: 2021-08-02T12:01:15.822472387Z ("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: 2021-08-02T12:01:15.822476362Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-02T12:01:15.822480361Z ("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: 2021-08-02T12:01:15.822484457Z [job score.cwl] completed permanentFail STDERR: 2021-08-02T12:01:15.822487758Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-02T12:01:15.822491170Z Traceback (most recent call last): STDERR: 2021-08-02T12:01:15.822494475Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-02T12:01:15.822498040Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-02T12:01:15.822501664Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-02T12:01:15.822505318Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-02T12:01:15.822508837Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-02T12:01:15.822512207Z return self.run(fileStore) STDERR: 2021-08-02T12:01:15.822515424Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-02T12:01:15.822519187Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-02T12:01:15.822525527Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-02T12:01:15.822528872Z ERROR:toil.worker:Exiting the worker because of a failed job on host 053b70656255 STDERR: 2021-08-02T12:01:15.822532572Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 to 0 STDERR: 2021-08-02T12:01:15.822537280Z <========= STDERR: 2021-08-02T12:01:15.822718325Z 053b70656255 2021-08-02 12:01:15,822 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 is completely failed STDERR: 2021-08-02T12:01:29.393122850Z 053b70656255 2021-08-02 12:01:29,392 MainThread INFO toil.leader: Finished toil run with 8 failed jobs. STDERR: 2021-08-02T12:01:29.393210944Z 053b70656255 2021-08-02 12:01:29,393 MainThread INFO toil.leader: Failed jobs at end of the run: 'CWLWorkflow' kind-CWLWorkflow/instance-ilye4g34 '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-c5b7nkhu '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-vfs2ry8i 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_validate.cwl/instance-s_w00veo '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-m5dpdjk4 '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-1qe4usyv '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-9jweq38g 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 STDERR: 2021-08-02T12:01:29.406714706Z Traceback (most recent call last): STDERR: 2021-08-02T12:01:29.406756558Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2021-08-02T12:01:29.406761831Z sys.exit(main()) STDERR: 2021-08-02T12:01:29.406765125Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2021-08-02T12:01:29.406769170Z outobj = toil.start(wf1) STDERR: 2021-08-02T12:01:29.406772249Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start STDERR: 2021-08-02T12:01:29.406775706Z return self._runMainLoop(rootJobGraph) STDERR: 2021-08-02T12:01:29.406779175Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop STDERR: 2021-08-02T12:01:29.406782876Z jobCache=self._jobCache).run() STDERR: 2021-08-02T12:01:29.406786277Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run STDERR: 2021-08-02T12:01:29.406789858Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2021-08-02T12:01:29.406794777Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/tmp3zhiutwr' contains 8 failed jobs: 'CWLWorkflow' kind-CWLWorkflow/instance-ilye4g34, '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-c5b7nkhu, '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-vfs2ry8i, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_validate.cwl/instance-s_w00veo, '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-m5dpdjk4, '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-1qe4usyv, '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-9jweq38g, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 STDERR: 2021-08-02T12:01:29.406803822Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 follows: STDERR: 2021-08-02T12:01:29.406807458Z =========> STDERR: 2021-08-02T12:01:29.406813800Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-02T12:01:29.406817391Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T12:01:29.406820977Z [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: 2021-08-02T12:01:29.406825076Z 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: 2021-08-02T12:01:29.406829274Z [job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr$ docker \ STDERR: 2021-08-02T12:01:29.406833554Z run \ STDERR: 2021-08-02T12:01:29.406836442Z -i \ STDERR: 2021-08-02T12:01:29.406962593Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr,target=/yKRORp \ STDERR: 2021-08-02T12:01:29.406969310Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x70mtw4_km,target=/tmp \ STDERR: 2021-08-02T12:01:29.406973422Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmp2l104iur.tmp,target=/var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig,readonly \ STDERR: 2021-08-02T12:01:29.406977844Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpn35q_ajc.tmp,target=/var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941,readonly \ STDERR: 2021-08-02T12:01:29.406989984Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpwi07pfbh.tmp,target=/var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T12:01:29.406994640Z --workdir=/yKRORp \ STDERR: 2021-08-02T12:01:29.406998394Z --read-only=true \ STDERR: 2021-08-02T12:01:29.407002032Z --user=0:0 \ STDERR: 2021-08-02T12:01:29.407005523Z --rm \ STDERR: 2021-08-02T12:01:29.407009226Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T12:01:29.407012659Z --env=HOME=/yKRORp \ STDERR: 2021-08-02T12:01:29.407029132Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x7jmukg_x5/20210802120113-604337.cid \ STDERR: 2021-08-02T12:01:29.407038452Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T12:01:29.407042170Z score.py \ STDERR: 2021-08-02T12:01:29.407045664Z --parent_id \ STDERR: 2021-08-02T12:01:29.407049222Z syn26020966 \ STDERR: 2021-08-02T12:01:29.407052936Z -s \ STDERR: 2021-08-02T12:01:29.407056493Z /var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig \ STDERR: 2021-08-02T12:01:29.407060252Z -p \ STDERR: 2021-08-02T12:01:29.407064016Z /var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941 \ STDERR: 2021-08-02T12:01:29.407067976Z -g \ STDERR: 2021-08-02T12:01:29.407071601Z /var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T12:01:29.407075312Z -c \ STDERR: 2021-08-02T12:01:29.407078711Z /work/CaPTk \ STDERR: 2021-08-02T12:01:29.407082465Z -o \ STDERR: 2021-08-02T12:01:29.407085977Z results.json STDERR: 2021-08-02T12:01:29.407089762Z INFO:cwltool:[job score.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr$ docker \ STDERR: 2021-08-02T12:01:29.407093852Z run \ STDERR: 2021-08-02T12:01:29.407097590Z -i \ STDERR: 2021-08-02T12:01:29.407101096Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tgq_i6kof/tmp-outkbxcgwdr,target=/yKRORp \ STDERR: 2021-08-02T12:01:29.407105618Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x70mtw4_km,target=/tmp \ STDERR: 2021-08-02T12:01:29.407109924Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmp2l104iur.tmp,target=/var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig,readonly \ STDERR: 2021-08-02T12:01:29.407114418Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpn35q_ajc.tmp,target=/var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941,readonly \ STDERR: 2021-08-02T12:01:29.407955931Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tmpwi07pfbh.tmp,target=/var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T12:01:29.407985931Z --workdir=/yKRORp \ STDERR: 2021-08-02T12:01:29.407989772Z --read-only=true \ STDERR: 2021-08-02T12:01:29.407993112Z --user=0:0 \ STDERR: 2021-08-02T12:01:29.407996965Z --rm \ STDERR: 2021-08-02T12:01:29.408000680Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T12:01:29.408004349Z --env=HOME=/yKRORp \ STDERR: 2021-08-02T12:01:29.408008116Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/node-679e43d7-7db7-4db0-8617-49ec0bc471ed-16349ee66b573b0d6cff3dbc6912349f/tmpyn5j63vw/4728f345-8e7e-4983-bc90-c78daa5cc3a0/tew6s49x7jmukg_x5/20210802120113-604337.cid \ STDERR: 2021-08-02T12:01:29.408012360Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T12:01:29.408016131Z score.py \ STDERR: 2021-08-02T12:01:29.408019479Z --parent_id \ STDERR: 2021-08-02T12:01:29.408023140Z syn26020966 \ STDERR: 2021-08-02T12:01:29.408027112Z -s \ STDERR: 2021-08-02T12:01:29.408030659Z /var/lib/cwl/stga486906c-a039-4585-9252-50c2b72e440f/.synapseConfig \ STDERR: 2021-08-02T12:01:29.408034505Z -p \ STDERR: 2021-08-02T12:01:29.408037832Z /var/lib/cwl/stg6bb758a9-816c-4be8-ad07-e7e9378d0e27/submission-9712941 \ STDERR: 2021-08-02T12:01:29.408041636Z -g \ STDERR: 2021-08-02T12:01:29.408045658Z /var/lib/cwl/stgf1ed5dc6-aebe-4b95-9f05-b504518cbfc2/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T12:01:29.408049372Z -c \ STDERR: 2021-08-02T12:01:29.408053232Z /work/CaPTk \ STDERR: 2021-08-02T12:01:29.408057015Z -o \ STDERR: 2021-08-02T12:01:29.408060449Z results.json STDERR: 2021-08-02T12:01:29.408064206Z Origin mismatch > 100100%' in axis '1'. STDERR: 2021-08-02T12:01:29.408068279Z 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: 2021-08-02T12:01:29.408072365Z Origin for input 1: STDERR: 2021-08-02T12:01:29.408075617Z [0, -239, 0] STDERR: 2021-08-02T12:01:29.408079148Z Origin for input 2: STDERR: 2021-08-02T12:01:29.408082633Z [0, 0, 0] STDERR: 2021-08-02T12:01:29.408086392Z /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: 2021-08-02T12:01:29.408090382Z warnings.warn(msg) STDERR: 2021-08-02T12:01:29.408094118Z Traceback (most recent call last): STDERR: 2021-08-02T12:01:29.408097705Z File "/usr/local/bin/score.py", line 141, in STDERR: 2021-08-02T12:01:29.408104472Z main() STDERR: 2021-08-02T12:01:29.408108080Z File "/usr/local/bin/score.py", line 115, in main STDERR: 2021-08-02T12:01:29.408111993Z results = score(preds, golds, args.captk_path) STDERR: 2021-08-02T12:01:29.408115700Z File "/usr/local/bin/score.py", line 102, in score STDERR: 2021-08-02T12:01:29.408120280Z run_captk(captk_path, pred, gold, tmp_output) STDERR: 2021-08-02T12:01:29.408124092Z File "/usr/local/bin/score.py", line 64, in run_captk STDERR: 2021-08-02T12:01:29.408127896Z subprocess.check_call(cmd) STDERR: 2021-08-02T12:01:29.408131460Z File "/usr/local/lib/python3.6/subprocess.py", line 291, in check_call STDERR: 2021-08-02T12:01:29.408135176Z raise CalledProcessError(retcode, cmd) STDERR: 2021-08-02T12:01:29.408139006Z 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: 2021-08-02T12:01:29.408143128Z [job score.cwl] Max memory used: 0MiB STDERR: 2021-08-02T12:01:29.408146664Z INFO:cwltool:[job score.cwl] Max memory used: 0MiB STDERR: 2021-08-02T12:01:29.408150314Z [job score.cwl] Job error: STDERR: 2021-08-02T12:01:29.408156029Z ("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: 2021-08-02T12:01:29.408160325Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2021-08-02T12:01:29.408164089Z ("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: 2021-08-02T12:01:29.408168376Z [job score.cwl] completed permanentFail STDERR: 2021-08-02T12:01:29.408172592Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2021-08-02T12:01:29.408176242Z Traceback (most recent call last): STDERR: 2021-08-02T12:01:29.408179947Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-02T12:01:29.408183808Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-02T12:01:29.408187932Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-02T12:01:29.408191806Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-02T12:01:29.408195569Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-02T12:01:29.408199329Z return self.run(fileStore) STDERR: 2021-08-02T12:01:29.408202973Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-02T12:01:29.408206792Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-02T12:01:29.408210441Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-02T12:01:29.408216942Z ERROR:toil.worker:Exiting the worker because of a failed job on host 053b70656255 STDERR: 2021-08-02T12:01:29.408272842Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/77e7f44c-6678-473f-b12c-f3b638c20275/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_77e7f44c-6678-473f-b12c-f3b638c20275_brats-dream-challenge-infra-main_score.cwl/instance-v7ydyhf9 to 0 STDERR: 2021-08-02T12:01:29.408279619Z <=========