Dear BraTS team, My submission (ID: 9713975) has encountered an error during scoring. This is the log file. Could you clarify where the issue is? Here is the detailed log file: STDERR: 2021-08-11T09:02:29.023238117Z 741245975c52 2021-08-11 09:02:29,022 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' STDERR: 2021-08-11T09:02:32.952342296Z 741245975c52 2021-08-11 09:02:32,952 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2021-08-11T09:02:32.952368228Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type STDERR: 2021-08-11T09:02:32.952372867Z ["null", "File"] may be STDERR: 2021-08-11T09:02:32.952376761Z incompatible STDERR: 2021-08-11T09:02:32.952393323Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:75:9: with sink 'input_file' of STDERR: 2021-08-11T09:02:32.952396959Z type "File" STDERR: 2021-08-11T09:02:32.952400178Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type STDERR: 2021-08-11T09:02:32.952403555Z ["null", "File"] may be STDERR: 2021-08-11T09:02:32.952406982Z incompatible STDERR: 2021-08-11T09:02:32.952409939Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:135:9: with sink 'input_file' of STDERR: 2021-08-11T09:02:32.952413035Z type "File" STDERR: 2021-08-11T09:02:34.348391615Z 741245975c52 2021-08-11 09:02:34,347 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-11T09:02:35.430394033Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp4qxgf7a4/worker_log.txt STDERR: 2021-08-11T09:02:36.023068205Z 741245975c52 2021-08-11 09:02:36,022 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2021-08-11T09:02:36.023858252Z 741245975c52 2021-08-11 09:02:36,023 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-8s450pls with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:02:36.023998236Z 741245975c52 2021-08-11 09:02:36,023 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-58iondka with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:02:36.024136290Z 741245975c52 2021-08-11 09:02:36,024 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_set_permissions.cwl/instance-ozaphoi4 with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:02:37.203860159Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmptxvviatq/worker_log.txt STDERR: 2021-08-11T09:02:37.274861921Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp4xd5cw9p/worker_log.txt STDERR: 2021-08-11T09:02:37.290624296Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmptumwtlp7/worker_log.txt STDERR: 2021-08-11T09:04:50.838842294Z 741245975c52 2021-08-11 09:04:50,837 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-8s450pls STDERR: 2021-08-11T09:05:13.110137628Z 741245975c52 2021-08-11 09:05:13,109 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_set_permissions.cwl/instance-ozaphoi4 STDERR: 2021-08-11T09:05:17.923784255Z 741245975c52 2021-08-11 09:05:17,923 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-58iondka STDERR: 2021-08-11T09:05:17.924404752Z 741245975c52 2021-08-11 09:05:17,924 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_validate.cwl/instance-ypx_e8ls with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:05:19.188894442Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp4uqopjor/worker_log.txt STDERR: 2021-08-11T09:06:37.330975484Z 741245975c52 2021-08-11 09:06:37,329 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_validate.cwl/instance-ypx_e8ls STDERR: 2021-08-11T09:06:37.331004927Z 741245975c52 2021-08-11 09:06:37,330 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-_ezceuiy with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:06:37.331021174Z 741245975c52 2021-08-11 09:06:37,330 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-x60mavrf with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:06:38.432267250Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp_5k17dm0/worker_log.txt STDERR: 2021-08-11T09:06:38.484449659Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpm0rl0th_/worker_log.txt STDERR: 2021-08-11T09:07:48.015176160Z 741245975c52 2021-08-11 09:07:48,014 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-_ezceuiy STDERR: 2021-08-11T09:07:50.362163948Z 741245975c52 2021-08-11 09:07:50,361 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-x60mavrf STDERR: 2021-08-11T09:07:50.363076144Z 741245975c52 2021-08-11 09:07:50,362 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-5nhnt0yf with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:07:51.306977865Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp7jdfoyz7/worker_log.txt STDERR: 2021-08-11T09:07:51.717953833Z 741245975c52 2021-08-11 09:07:51,717 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-5nhnt0yf STDERR: 2021-08-11T09:07:51.718756454Z 741245975c52 2021-08-11 09:07:51,718 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score.cwl/instance-t2o2bcy5 with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:07:52.617209098Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp4mdq2lcu/worker_log.txt STDERR: 2021-08-11T09:09:40.344759341Z 741245975c52 2021-08-11 09:09:40,344 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score.cwl/instance-t2o2bcy5 STDERR: 2021-08-11T09:09:40.345742269Z 741245975c52 2021-08-11 09:09:40,345 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-g2artjgt with job batch system ID: 9 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:09:40.345913329Z 741245975c52 2021-08-11 09:09:40,345 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score_email.cwl/instance-5hu5a9i_ with job batch system ID: 10 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:09:41.444683678Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmp8512gzne/worker_log.txt STDERR: 2021-08-11T09:09:41.538000460Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpg3du7yfm/worker_log.txt STDERR: 2021-08-11T09:11:02.682414886Z 741245975c52 2021-08-11 09:11:02,681 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-g2artjgt STDERR: 2021-08-11T09:11:02.693829282Z 741245975c52 2021-08-11 09:11:02,693 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score_email.cwl/instance-5hu5a9i_ STDERR: 2021-08-11T09:11:02.694483019Z 741245975c52 2021-08-11 09:11:02,694 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-y2s1u6st with job batch system ID: 11 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-11T09:11:03.972102820Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpegnvabzv/worker_log.txt STDERR: 2021-08-11T09:11:04.391064208Z 741245975c52 2021-08-11 09:11:04,390 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-y2s1u6st STDERR: 2021-08-11T09:11:04.392519140Z 741245975c52 2021-08-11 09:11:04,391 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: '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-y2s1u6st STDERR: 2021-08-11T09:11:04.392536059Z 741245975c52 2021-08-11 09:11:04,391 MainThread WARNING toil.leader: Log from job kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-y2s1u6st follows: STDERR: 2021-08-11T09:11:04.392540683Z =========> STDERR: 2021-08-11T09:11:04.392544340Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-11T09:11:04.392547889Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-11T09:11:04.392551635Z Failed to evaluate expression: STDERR: 2021-08-11T09:11:04.392554751Z Expression evaluation error: STDERR: 2021-08-11T09:11:04.392557947Z Expecting value: line 1 column 1 (char 0) STDERR: 2021-08-11T09:11:04.392561199Z script was: STDERR: 2021-08-11T09:11:04.392564535Z 01 "use strict"; STDERR: 2021-08-11T09:11:04.392567799Z 02 var inputs = { STDERR: 2021-08-11T09:11:04.392571000Z 03 "status": "INVALID", STDERR: 2021-08-11T09:11:04.392574514Z 04 "previous_annotation_finished": true, STDERR: 2021-08-11T09:11:04.392578224Z 05 "previous_email_finished": true STDERR: 2021-08-11T09:11:04.392581504Z 06 }; STDERR: 2021-08-11T09:11:04.392584600Z 07 var self = null; STDERR: 2021-08-11T09:11:04.392587772Z 08 var runtime = { STDERR: 2021-08-11T09:11:04.392590933Z 09 "cores": 1, STDERR: 2021-08-11T09:11:04.392594245Z 10 "ram": 100.0, STDERR: 2021-08-11T09:11:04.392597528Z 11 "tmpdirSize": 1024, STDERR: 2021-08-11T09:11:04.392600851Z 12 "outdirSize": 0.95367431640625, STDERR: 2021-08-11T09:11:04.392604313Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/tmpmupxdrsj", STDERR: 2021-08-11T09:11:04.392608156Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpegnvabzv/308b47c8-b00c-4473-8ee1-d5c1b50bcc04/tl5yc4ww3/tmp-outiji0s0ri" STDERR: 2021-08-11T09:11:04.392612281Z 15 }; STDERR: 2021-08-11T09:11:04.392615590Z 16 (function(){ STDERR: 2021-08-11T09:11:04.392618830Z 17 if(inputs.status == "INVALID"){ STDERR: 2021-08-11T09:11:04.392622142Z 18 throw 'invalid submission'; STDERR: 2021-08-11T09:11:04.392625331Z 19 } else { STDERR: 2021-08-11T09:11:04.392628442Z 20 return {finished: true}; STDERR: 2021-08-11T09:11:04.392631641Z 21 } STDERR: 2021-08-11T09:11:04.392634751Z 22 })() STDERR: 2021-08-11T09:11:04.392637809Z stdout was: '' STDERR: 2021-08-11T09:11:04.392647361Z stderr was: 'invalid submission' STDERR: 2021-08-11T09:11:04.392650649Z STDERR: 2021-08-11T09:11:04.392653820Z WARNING:cwltool:Failed to evaluate expression: STDERR: 2021-08-11T09:11:04.392657081Z Expression evaluation error: STDERR: 2021-08-11T09:11:04.392660201Z Expecting value: line 1 column 1 (char 0) STDERR: 2021-08-11T09:11:04.392663451Z script was: STDERR: 2021-08-11T09:11:04.392666498Z 01 "use strict"; STDERR: 2021-08-11T09:11:04.392669757Z 02 var inputs = { STDERR: 2021-08-11T09:11:04.392672883Z 03 "status": "INVALID", STDERR: 2021-08-11T09:11:04.392676150Z 04 "previous_annotation_finished": true, STDERR: 2021-08-11T09:11:04.392679492Z 05 "previous_email_finished": true STDERR: 2021-08-11T09:11:04.392682957Z 06 }; STDERR: 2021-08-11T09:11:04.392686934Z 07 var self = null; STDERR: 2021-08-11T09:11:04.392690134Z 08 var runtime = { STDERR: 2021-08-11T09:11:04.392693185Z 09 "cores": 1, STDERR: 2021-08-11T09:11:04.392696384Z 10 "ram": 100.0, STDERR: 2021-08-11T09:11:04.392699614Z 11 "tmpdirSize": 1024, STDERR: 2021-08-11T09:11:04.392702853Z 12 "outdirSize": 0.95367431640625, STDERR: 2021-08-11T09:11:04.392706199Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/tmpmupxdrsj", STDERR: 2021-08-11T09:11:04.392710057Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpegnvabzv/308b47c8-b00c-4473-8ee1-d5c1b50bcc04/tl5yc4ww3/tmp-outiji0s0ri" STDERR: 2021-08-11T09:11:04.392714138Z 15 }; STDERR: 2021-08-11T09:11:04.392717426Z 16 (function(){ STDERR: 2021-08-11T09:11:04.392720620Z 17 if(inputs.status == "INVALID"){ STDERR: 2021-08-11T09:11:04.392724090Z 18 throw 'invalid submission'; STDERR: 2021-08-11T09:11:04.392727310Z 19 } else { STDERR: 2021-08-11T09:11:04.392730499Z 20 return {finished: true}; STDERR: 2021-08-11T09:11:04.392733649Z 21 } STDERR: 2021-08-11T09:11:04.392736796Z 22 })() STDERR: 2021-08-11T09:11:04.392739921Z stdout was: '' STDERR: 2021-08-11T09:11:04.392742975Z stderr was: 'invalid submission' STDERR: 2021-08-11T09:11:04.392746187Z STDERR: 2021-08-11T09:11:04.392749217Z Traceback (most recent call last): STDERR: 2021-08-11T09:11:04.392752548Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-11T09:11:04.392756418Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-11T09:11:04.392759801Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-11T09:11:04.392763238Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-11T09:11:04.392769296Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-11T09:11:04.392772858Z return self.run(fileStore) STDERR: 2021-08-11T09:11:04.392776061Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-11T09:11:04.392779521Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-11T09:11:04.392782762Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-11T09:11:04.392785980Z ERROR:toil.worker:Exiting the worker because of a failed job on host 741245975c52 STDERR: 2021-08-11T09:11:04.392789504Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of 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-y2s1u6st with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-y2s1u6st to 0 STDERR: 2021-08-11T09:11:04.392794408Z <========= STDERR: 2021-08-11T09:11:04.392837500Z 741245975c52 2021-08-11 09:11:04,392 MainThread WARNING toil.leader: 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-y2s1u6st with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-y2s1u6st is completely failed STDERR: 2021-08-11T09:11:22.126056589Z 741245975c52 2021-08-11 09:11:22,125 MainThread INFO toil.leader: Finished toil run with 11 failed jobs. STDERR: 2021-08-11T09:11:22.126121779Z 741245975c52 2021-08-11 09:11:22,125 MainThread INFO toil.leader: Failed jobs at end of the run: '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-58iondka '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-g2artjgt '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-x60mavrf 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_validate.cwl/instance-ypx_e8ls 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score.cwl/instance-t2o2bcy5 '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-8s450pls '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-5nhnt0yf 'CWLWorkflow' kind-CWLWorkflow/instance-ovaghm96 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score_email.cwl/instance-5hu5a9i_ '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-y2s1u6st '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-_ezceuiy STDERR: 2021-08-11T09:11:22.138194025Z Traceback (most recent call last): STDERR: 2021-08-11T09:11:22.138223980Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2021-08-11T09:11:22.138229023Z sys.exit(main()) STDERR: 2021-08-11T09:11:22.138232567Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2021-08-11T09:11:22.138236471Z outobj = toil.start(wf1) STDERR: 2021-08-11T09:11:22.138240037Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start STDERR: 2021-08-11T09:11:22.138243860Z return self._runMainLoop(rootJobGraph) STDERR: 2021-08-11T09:11:22.138247464Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop STDERR: 2021-08-11T09:11:22.138251512Z jobCache=self._jobCache).run() STDERR: 2021-08-11T09:11:22.138255048Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run STDERR: 2021-08-11T09:11:22.138259012Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2021-08-11T09:11:22.138264480Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/tmpydpwejab' contains 11 failed jobs: '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-58iondka, '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-g2artjgt, '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-x60mavrf, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_validate.cwl/instance-ypx_e8ls, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score.cwl/instance-t2o2bcy5, '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-8s450pls, '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-5nhnt0yf, 'CWLWorkflow' kind-CWLWorkflow/instance-ovaghm96, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_80f45323-8475-4cc4-bac3-5becdba30c3e_brats-dream-challenge-infra-main_score_email.cwl/instance-5hu5a9i_, '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-y2s1u6st, '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-_ezceuiy STDERR: 2021-08-11T09:11:22.138288517Z Log from 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-y2s1u6st follows: STDERR: 2021-08-11T09:11:22.138292754Z =========> STDERR: 2021-08-11T09:11:22.138296206Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-11T09:11:22.138300037Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-11T09:11:22.138303602Z Failed to evaluate expression: STDERR: 2021-08-11T09:11:22.138349507Z Expression evaluation error: STDERR: 2021-08-11T09:11:22.138354429Z Expecting value: line 1 column 1 (char 0) STDERR: 2021-08-11T09:11:22.138358213Z script was: STDERR: 2021-08-11T09:11:22.138361442Z 01 "use strict"; STDERR: 2021-08-11T09:11:22.138365085Z 02 var inputs = { STDERR: 2021-08-11T09:11:22.138369000Z 03 "status": "INVALID", STDERR: 2021-08-11T09:11:22.138372867Z 04 "previous_annotation_finished": true, STDERR: 2021-08-11T09:11:22.138376782Z 05 "previous_email_finished": true STDERR: 2021-08-11T09:11:22.138380453Z 06 }; STDERR: 2021-08-11T09:11:22.138384175Z 07 var self = null; STDERR: 2021-08-11T09:11:22.138387858Z 08 var runtime = { STDERR: 2021-08-11T09:11:22.138391755Z 09 "cores": 1, STDERR: 2021-08-11T09:11:22.138395363Z 10 "ram": 100.0, STDERR: 2021-08-11T09:11:22.138399000Z 11 "tmpdirSize": 1024, STDERR: 2021-08-11T09:11:22.138402652Z 12 "outdirSize": 0.95367431640625, STDERR: 2021-08-11T09:11:22.138406301Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/tmpmupxdrsj", STDERR: 2021-08-11T09:11:22.138410407Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpegnvabzv/308b47c8-b00c-4473-8ee1-d5c1b50bcc04/tl5yc4ww3/tmp-outiji0s0ri" STDERR: 2021-08-11T09:11:22.138418860Z 15 }; STDERR: 2021-08-11T09:11:22.138422297Z 16 (function(){ STDERR: 2021-08-11T09:11:22.138425913Z 17 if(inputs.status == "INVALID"){ STDERR: 2021-08-11T09:11:22.138430222Z 18 throw 'invalid submission'; STDERR: 2021-08-11T09:11:22.138433813Z 19 } else { STDERR: 2021-08-11T09:11:22.138437129Z 20 return {finished: true}; STDERR: 2021-08-11T09:11:22.138440787Z 21 } STDERR: 2021-08-11T09:11:22.138444423Z 22 })() STDERR: 2021-08-11T09:11:22.138447796Z stdout was: '' STDERR: 2021-08-11T09:11:22.138451259Z stderr was: 'invalid submission' STDERR: 2021-08-11T09:11:22.138454972Z STDERR: 2021-08-11T09:11:22.138458267Z WARNING:cwltool:Failed to evaluate expression: STDERR: 2021-08-11T09:11:22.138461900Z Expression evaluation error: STDERR: 2021-08-11T09:11:22.138465357Z Expecting value: line 1 column 1 (char 0) STDERR: 2021-08-11T09:11:22.138468976Z script was: STDERR: 2021-08-11T09:11:22.138472399Z 01 "use strict"; STDERR: 2021-08-11T09:11:22.138476095Z 02 var inputs = { STDERR: 2021-08-11T09:11:22.138479491Z 03 "status": "INVALID", STDERR: 2021-08-11T09:11:22.138483068Z 04 "previous_annotation_finished": true, STDERR: 2021-08-11T09:11:22.138486819Z 05 "previous_email_finished": true STDERR: 2021-08-11T09:11:22.138490699Z 06 }; STDERR: 2021-08-11T09:11:22.138494322Z 07 var self = null; STDERR: 2021-08-11T09:11:22.138498245Z 08 var runtime = { STDERR: 2021-08-11T09:11:22.138501416Z 09 "cores": 1, STDERR: 2021-08-11T09:11:22.138505077Z 10 "ram": 100.0, STDERR: 2021-08-11T09:11:22.138511135Z 11 "tmpdirSize": 1024, STDERR: 2021-08-11T09:11:22.138514857Z 12 "outdirSize": 0.95367431640625, STDERR: 2021-08-11T09:11:22.138519016Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/tmpmupxdrsj", STDERR: 2021-08-11T09:11:22.138523327Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/80f45323-8475-4cc4-bac3-5becdba30c3e/node-2ad75fda-782f-42bd-b429-f4f712ee5096-16349ee66b573b0d6cff3dbc6912349f/tmpegnvabzv/308b47c8-b00c-4473-8ee1-d5c1b50bcc04/tl5yc4ww3/tmp-outiji0s0ri" STDERR: 2021-08-11T09:11:22.138527617Z 15 }; STDERR: 2021-08-11T09:11:22.138531121Z 16 (function(){ STDERR: 2021-08-11T09:11:22.138534743Z 17 if(inputs.status == "INVALID"){ STDERR: 2021-08-11T09:11:22.138538416Z 18 throw 'invalid submission'; STDERR: 2021-08-11T09:11:22.138541888Z 19 } else { STDERR: 2021-08-11T09:11:22.138545571Z 20 return {finished: true}; STDERR: 2021-08-11T09:11:22.138552025Z 21 } STDERR: 2021-08-11T09:11:22.138555490Z 22 })() STDERR: 2021-08-11T09:11:22.138558913Z stdout was: '' STDERR: 2021-08-11T09:11:22.138562467Z stderr was: 'invalid submission' STDERR: 2021-08-11T09:11:22.138566439Z STDERR: 2021-08-11T09:11:22.138570621Z Traceback (most recent call last): STDERR: 2021-08-11T09:11:22.138574296Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-11T09:11:22.138578119Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-11T09:11:22.138581822Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-11T09:11:22.138585534Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-11T09:11:22.138589079Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-11T09:11:22.138592699Z return self.run(fileStore) STDERR: 2021-08-11T09:11:22.138596333Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-11T09:11:22.138599879Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-11T09:11:22.138603590Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-11T09:11:22.138607180Z ERROR:toil.worker:Exiting the worker because of a failed job on host 741245975c52 STDERR: 2021-08-11T09:11:22.138611112Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of 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-y2s1u6st with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-y2s1u6st to 0 STDERR: 2021-08-11T09:11:22.138615486Z <=========