STDERR: 2021-08-19T03:33:43.703067564Z 11dba82f35de 2021-08-19 03:33:43,702 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-19T03:33:47.604682306Z 11dba82f35de 2021-08-19 03:33:47,604 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2021-08-19T03:33:47.604725959Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-19T03:33:47.604730002Z ["null", "File"] may be
STDERR: 2021-08-19T03:33:47.604733438Z incompatible
STDERR: 2021-08-19T03:33:47.604736789Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:135:9: with sink 'input_file' of
STDERR: 2021-08-19T03:33:47.604739734Z type "File"
STDERR: 2021-08-19T03:33:47.604742891Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-19T03:33:47.604745878Z ["null", "File"] may be
STDERR: 2021-08-19T03:33:47.604749214Z incompatible
STDERR: 2021-08-19T03:33:47.604752102Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:75:9: with sink 'input_file' of
STDERR: 2021-08-19T03:33:47.604754831Z type "File"
STDERR: 2021-08-19T03:33:49.872421954Z 11dba82f35de 2021-08-19 03:33:49,872 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-19T03:33:50.503423953Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmp0yfy4l_p/worker_log.txt
STDERR: 2021-08-19T03:33:50.868760731Z 11dba82f35de 2021-08-19 03:33:50,868 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2021-08-19T03:33:50.869275898Z 11dba82f35de 2021-08-19 03:33:50,869 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-b4se_tru with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:33:50.869345327Z 11dba82f35de 2021-08-19 03:33:50,869 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-9rugm4h0 with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:33:50.869418853Z 11dba82f35de 2021-08-19 03:33:50,869 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-ljagdwpv with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:33:51.545839716Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpk71ioycf/worker_log.txt
STDERR: 2021-08-19T03:33:51.576990331Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpagx57noo/worker_log.txt
STDERR: 2021-08-19T03:33:51.587429530Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpbkti5y2i/worker_log.txt
STDERR: 2021-08-19T03:39:01.043816407Z 11dba82f35de 2021-08-19 03:39:01,042 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-9rugm4h0
STDERR: 2021-08-19T03:39:05.996470584Z 11dba82f35de 2021-08-19 03:39:05,996 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-ljagdwpv
STDERR: 2021-08-19T03:39:57.606665182Z 11dba82f35de 2021-08-19 03:39:57,606 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-b4se_tru
STDERR: 2021-08-19T03:39:57.607114912Z 11dba82f35de 2021-08-19 03:39:57,607 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_validate.cwl/instance-i58abpqi with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:39:58.176718422Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpih6re_l2/worker_log.txt
STDERR: 2021-08-19T03:43:28.461426864Z 11dba82f35de 2021-08-19 03:43:28,461 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_validate.cwl/instance-i58abpqi
STDERR: 2021-08-19T03:43:28.461926033Z 11dba82f35de 2021-08-19 03:43:28,461 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-647zndei with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:43:28.461978650Z 11dba82f35de 2021-08-19 03:43:28,461 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-aqz03nvj with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:43:29.080620570Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmp4007i7bo/worker_log.txt
STDERR: 2021-08-19T03:43:29.098601249Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmp1ggueejf/worker_log.txt
STDERR: 2021-08-19T03:47:12.578967331Z 11dba82f35de 2021-08-19 03:47:12,578 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-aqz03nvj
STDERR: 2021-08-19T03:47:21.957825165Z 11dba82f35de 2021-08-19 03:47:21,957 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-647zndei
STDERR: 2021-08-19T03:47:21.958254371Z 11dba82f35de 2021-08-19 03:47:21,958 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-qvvwkg0u with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:47:22.503931885Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpsw47esgl/worker_log.txt
STDERR: 2021-08-19T03:47:23.005790651Z 11dba82f35de 2021-08-19 03:47:23,005 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-qvvwkg0u
STDERR: 2021-08-19T03:47:23.006343522Z 11dba82f35de 2021-08-19 03:47:23,006 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score.cwl/instance-11i5zwgb with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:47:23.532588382Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmp8epixgd_/worker_log.txt
STDERR: 2021-08-19T03:50:02.829274690Z 11dba82f35de 2021-08-19 03:50:02,828 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score.cwl/instance-11i5zwgb
STDERR: 2021-08-19T03:50:02.830426502Z 11dba82f35de 2021-08-19 03:50:02,830 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score_email.cwl/instance-2w0jly15 with job batch system ID: 9 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:50:02.830567594Z 11dba82f35de 2021-08-19 03:50:02,830 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-jyrw_9nd with job batch system ID: 10 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:50:03.474880892Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmphk9cgrv6/worker_log.txt
STDERR: 2021-08-19T03:50:03.535968690Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmp79izf3qn/worker_log.txt
STDERR: 2021-08-19T03:54:24.776840855Z 11dba82f35de 2021-08-19 03:54:24,776 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-jyrw_9nd
STDERR: 2021-08-19T03:54:55.076649833Z 11dba82f35de 2021-08-19 03:54:55,076 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score_email.cwl/instance-2w0jly15
STDERR: 2021-08-19T03:54:55.077331917Z 11dba82f35de 2021-08-19 03:54:55,077 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-gmfbdjrj with job batch system ID: 11 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-19T03:54:55.690378639Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpul40jwgo/worker_log.txt
STDERR: 2021-08-19T03:54:56.044397138Z 11dba82f35de 2021-08-19 03:54:56,043 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-gmfbdjrj
STDERR: 2021-08-19T03:54:56.044984808Z 11dba82f35de 2021-08-19 03:54:56,044 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-gmfbdjrj
STDERR: 2021-08-19T03:54:56.045215892Z 11dba82f35de 2021-08-19 03:54:56,045 MainThread WARNING toil.leader: Log from job kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-gmfbdjrj follows:
STDERR: 2021-08-19T03:54:56.045226413Z =========>
STDERR: 2021-08-19T03:54:56.045229658Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2021-08-19T03:54:56.045232373Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-19T03:54:56.045234993Z Failed to evaluate expression:
STDERR: 2021-08-19T03:54:56.045237478Z Expression evaluation error:
STDERR: 2021-08-19T03:54:56.045239867Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-19T03:54:56.045242259Z script was:
STDERR: 2021-08-19T03:54:56.045244519Z 01 "use strict";
STDERR: 2021-08-19T03:54:56.045247325Z 02 var inputs = {
STDERR: 2021-08-19T03:54:56.045250792Z 03 "status": "INVALID",
STDERR: 2021-08-19T03:54:56.045253183Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-19T03:54:56.045255792Z 05 "previous_email_finished": true
STDERR: 2021-08-19T03:54:56.045258492Z 06 };
STDERR: 2021-08-19T03:54:56.045260949Z 07 var self = null;
STDERR: 2021-08-19T03:54:56.045263319Z 08 var runtime = {
STDERR: 2021-08-19T03:54:56.045265908Z 09 "cores": 1,
STDERR: 2021-08-19T03:54:56.045268365Z 10 "ram": 100.0,
STDERR: 2021-08-19T03:54:56.045270857Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-19T03:54:56.045272972Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-19T03:54:56.045275258Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/tmp7tat_xgf",
STDERR: 2021-08-19T03:54:56.045278065Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpul40jwgo/34ed693c-c4c1-4680-ae97-5c20ad0d0541/tgo6zgfmb/tmp-outqh3zhq1q"
STDERR: 2021-08-19T03:54:56.045281749Z 15 };
STDERR: 2021-08-19T03:54:56.045284559Z 16 (function(){
STDERR: 2021-08-19T03:54:56.045287096Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-19T03:54:56.045289792Z 18 throw 'invalid submission';
STDERR: 2021-08-19T03:54:56.045292327Z 19 } else {
STDERR: 2021-08-19T03:54:56.045294642Z 20 return {finished: true};
STDERR: 2021-08-19T03:54:56.045297131Z 21 }
STDERR: 2021-08-19T03:54:56.045299579Z 22 })()
STDERR: 2021-08-19T03:54:56.045302325Z stdout was: ''
STDERR: 2021-08-19T03:54:56.045312254Z stderr was: 'invalid submission'
STDERR: 2021-08-19T03:54:56.045314871Z
STDERR: 2021-08-19T03:54:56.045317129Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2021-08-19T03:54:56.045319605Z Expression evaluation error:
STDERR: 2021-08-19T03:54:56.045321948Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-19T03:54:56.045324649Z script was:
STDERR: 2021-08-19T03:54:56.045326928Z 01 "use strict";
STDERR: 2021-08-19T03:54:56.045329410Z 02 var inputs = {
STDERR: 2021-08-19T03:54:56.045331888Z 03 "status": "INVALID",
STDERR: 2021-08-19T03:54:56.045334459Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-19T03:54:56.045336915Z 05 "previous_email_finished": true
STDERR: 2021-08-19T03:54:56.045339430Z 06 };
STDERR: 2021-08-19T03:54:56.045341746Z 07 var self = null;
STDERR: 2021-08-19T03:54:56.045344131Z 08 var runtime = {
STDERR: 2021-08-19T03:54:56.045346457Z 09 "cores": 1,
STDERR: 2021-08-19T03:54:56.045348898Z 10 "ram": 100.0,
STDERR: 2021-08-19T03:54:56.045351548Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-19T03:54:56.045354145Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-19T03:54:56.045356729Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/tmp7tat_xgf",
STDERR: 2021-08-19T03:54:56.045360228Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpul40jwgo/34ed693c-c4c1-4680-ae97-5c20ad0d0541/tgo6zgfmb/tmp-outqh3zhq1q"
STDERR: 2021-08-19T03:54:56.045363382Z 15 };
STDERR: 2021-08-19T03:54:56.045365637Z 16 (function(){
STDERR: 2021-08-19T03:54:56.045367919Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-19T03:54:56.045370391Z 18 throw 'invalid submission';
STDERR: 2021-08-19T03:54:56.045372746Z 19 } else {
STDERR: 2021-08-19T03:54:56.045375054Z 20 return {finished: true};
STDERR: 2021-08-19T03:54:56.045377407Z 21 }
STDERR: 2021-08-19T03:54:56.045379706Z 22 })()
STDERR: 2021-08-19T03:54:56.045381959Z stdout was: ''
STDERR: 2021-08-19T03:54:56.045384233Z stderr was: 'invalid submission'
STDERR: 2021-08-19T03:54:56.045386878Z
STDERR: 2021-08-19T03:54:56.045389329Z Traceback (most recent call last):
STDERR: 2021-08-19T03:54:56.045391839Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2021-08-19T03:54:56.045394502Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2021-08-19T03:54:56.045397020Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2021-08-19T03:54:56.045399533Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2021-08-19T03:54:56.045404513Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run
STDERR: 2021-08-19T03:54:56.045407149Z return self.run(fileStore)
STDERR: 2021-08-19T03:54:56.045409558Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2021-08-19T03:54:56.045412686Z raise cwltool.errors.WorkflowException(status)
STDERR: 2021-08-19T03:54:56.045415240Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2021-08-19T03:54:56.045417656Z ERROR:toil.worker:Exiting the worker because of a failed job on host 11dba82f35de
STDERR: 2021-08-19T03:54:56.045420300Z 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-gmfbdjrj with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-gmfbdjrj to 0
STDERR: 2021-08-19T03:54:56.045424027Z <=========
STDERR: 2021-08-19T03:54:56.045478690Z 11dba82f35de 2021-08-19 03:54:56,045 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-gmfbdjrj with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-gmfbdjrj is completely failed
STDERR: 2021-08-19T03:55:13.579648394Z 11dba82f35de 2021-08-19 03:55:13,579 MainThread INFO toil.leader: Finished toil run with 11 failed jobs.
STDERR: 2021-08-19T03:55:13.579676565Z 11dba82f35de 2021-08-19 03:55:13,579 MainThread INFO toil.leader: Failed jobs at end of the run: '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-gmfbdjrj 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score_email.cwl/instance-2w0jly15 'CWLWorkflow' kind-CWLWorkflow/instance-plg_9ttu 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_validate.cwl/instance-i58abpqi '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-9rugm4h0 '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-jyrw_9nd '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-647zndei '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-b4se_tru 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score.cwl/instance-11i5zwgb '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-aqz03nvj '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-qvvwkg0u
STDERR: 2021-08-19T03:55:13.593894556Z Traceback (most recent call last):
STDERR: 2021-08-19T03:55:13.593921329Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2021-08-19T03:55:13.593925361Z sys.exit(main())
STDERR: 2021-08-19T03:55:13.593928008Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2021-08-19T03:55:13.593930780Z outobj = toil.start(wf1)
STDERR: 2021-08-19T03:55:13.593933417Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start
STDERR: 2021-08-19T03:55:13.593936196Z return self._runMainLoop(rootJobGraph)
STDERR: 2021-08-19T03:55:13.593938684Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop
STDERR: 2021-08-19T03:55:13.593941438Z jobCache=self._jobCache).run()
STDERR: 2021-08-19T03:55:13.593943999Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run
STDERR: 2021-08-19T03:55:13.593946721Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2021-08-19T03:55:13.593951617Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/tmpokdmt_33' contains 11 failed jobs: '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-gmfbdjrj, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score_email.cwl/instance-2w0jly15, 'CWLWorkflow' kind-CWLWorkflow/instance-plg_9ttu, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_validate.cwl/instance-i58abpqi, '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-9rugm4h0, '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-jyrw_9nd, '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-647zndei, '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-b4se_tru, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_a726e9f8-8320-4f10-95ea-63403f9e9832_brats-dream-challenge-infra-main_score.cwl/instance-11i5zwgb, '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-aqz03nvj, '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-qvvwkg0u
STDERR: 2021-08-19T03:55:13.593971967Z 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-gmfbdjrj follows:
STDERR: 2021-08-19T03:55:13.593975296Z =========>
STDERR: 2021-08-19T03:55:13.593977700Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2021-08-19T03:55:13.593980421Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-19T03:55:13.593983018Z Failed to evaluate expression:
STDERR: 2021-08-19T03:55:13.593985888Z Expression evaluation error:
STDERR: 2021-08-19T03:55:13.593988400Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-19T03:55:13.593991012Z script was:
STDERR: 2021-08-19T03:55:13.593993226Z 01 "use strict";
STDERR: 2021-08-19T03:55:13.593995674Z 02 var inputs = {
STDERR: 2021-08-19T03:55:13.593997893Z 03 "status": "INVALID",
STDERR: 2021-08-19T03:55:13.594000411Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-19T03:55:13.594002673Z 05 "previous_email_finished": true
STDERR: 2021-08-19T03:55:13.594005160Z 06 };
STDERR: 2021-08-19T03:55:13.594007632Z 07 var self = null;
STDERR: 2021-08-19T03:55:13.594010253Z 08 var runtime = {
STDERR: 2021-08-19T03:55:13.594012716Z 09 "cores": 1,
STDERR: 2021-08-19T03:55:13.594015753Z 10 "ram": 100.0,
STDERR: 2021-08-19T03:55:13.594018400Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-19T03:55:13.594020923Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-19T03:55:13.594023396Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/tmp7tat_xgf",
STDERR: 2021-08-19T03:55:13.594028831Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpul40jwgo/34ed693c-c4c1-4680-ae97-5c20ad0d0541/tgo6zgfmb/tmp-outqh3zhq1q"
STDERR: 2021-08-19T03:55:13.594032414Z 15 };
STDERR: 2021-08-19T03:55:13.594035002Z 16 (function(){
STDERR: 2021-08-19T03:55:13.594037429Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-19T03:55:13.594040359Z 18 throw 'invalid submission';
STDERR: 2021-08-19T03:55:13.594043424Z 19 } else {
STDERR: 2021-08-19T03:55:13.594045891Z 20 return {finished: true};
STDERR: 2021-08-19T03:55:13.594048404Z 21 }
STDERR: 2021-08-19T03:55:13.594050764Z 22 })()
STDERR: 2021-08-19T03:55:13.594053033Z stdout was: ''
STDERR: 2021-08-19T03:55:13.594055366Z stderr was: 'invalid submission'
STDERR: 2021-08-19T03:55:13.594057677Z
STDERR: 2021-08-19T03:55:13.594059956Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2021-08-19T03:55:13.594062200Z Expression evaluation error:
STDERR: 2021-08-19T03:55:13.594064778Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-19T03:55:13.594067231Z script was:
STDERR: 2021-08-19T03:55:13.594069860Z 01 "use strict";
STDERR: 2021-08-19T03:55:13.594072428Z 02 var inputs = {
STDERR: 2021-08-19T03:55:13.594075070Z 03 "status": "INVALID",
STDERR: 2021-08-19T03:55:13.594077647Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-19T03:55:13.594080170Z 05 "previous_email_finished": true
STDERR: 2021-08-19T03:55:13.594082667Z 06 };
STDERR: 2021-08-19T03:55:13.594085109Z 07 var self = null;
STDERR: 2021-08-19T03:55:13.594087375Z 08 var runtime = {
STDERR: 2021-08-19T03:55:13.594089771Z 09 "cores": 1,
STDERR: 2021-08-19T03:55:13.594092299Z 10 "ram": 100.0,
STDERR: 2021-08-19T03:55:13.594094948Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-19T03:55:13.594097484Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-19T03:55:13.594100262Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/tmp7tat_xgf",
STDERR: 2021-08-19T03:55:13.594103174Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/a726e9f8-8320-4f10-95ea-63403f9e9832/node-7b16c6e3-1916-44ee-846c-d4f99b191226-16349ee66b573b0d6cff3dbc6912349f/tmpul40jwgo/34ed693c-c4c1-4680-ae97-5c20ad0d0541/tgo6zgfmb/tmp-outqh3zhq1q"
STDERR: 2021-08-19T03:55:13.594106304Z 15 };
STDERR: 2021-08-19T03:55:13.594108565Z 16 (function(){
STDERR: 2021-08-19T03:55:13.594111190Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-19T03:55:13.594113782Z 18 throw 'invalid submission';
STDERR: 2021-08-19T03:55:13.594116308Z 19 } else {
STDERR: 2021-08-19T03:55:13.594118900Z 20 return {finished: true};
STDERR: 2021-08-19T03:55:13.594125799Z 21 }
STDERR: 2021-08-19T03:55:13.594128111Z 22 })()
STDERR: 2021-08-19T03:55:13.594130480Z stdout was: ''
STDERR: 2021-08-19T03:55:13.594132841Z stderr was: 'invalid submission'
STDERR: 2021-08-19T03:55:13.594135434Z
STDERR: 2021-08-19T03:55:13.594138553Z Traceback (most recent call last):
STDERR: 2021-08-19T03:55:13.594141084Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2021-08-19T03:55:13.594143819Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2021-08-19T03:55:13.594146422Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2021-08-19T03:55:13.594148961Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2021-08-19T03:55:13.594151425Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run
STDERR: 2021-08-19T03:55:13.594153992Z return self.run(fileStore)
STDERR: 2021-08-19T03:55:13.594156914Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2021-08-19T03:55:13.594159440Z raise cwltool.errors.WorkflowException(status)
STDERR: 2021-08-19T03:55:13.594161979Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2021-08-19T03:55:13.594164635Z ERROR:toil.worker:Exiting the worker because of a failed job on host 11dba82f35de
STDERR: 2021-08-19T03:55:13.594167489Z 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-gmfbdjrj with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-gmfbdjrj to 0
STDERR: 2021-08-19T03:55:13.594170947Z <=========
Created by PARVEZ AHMAD parvezamu Thanks Dear @parvezamu ,
Your submission, 9714734, cannot be properly scored due to an origin mismatch between your predictions and the references:
```
Origin for input 1:
[0, -239, 0]
Origin for input 2:
[0, 0, 0]
Origin mismatch > 100%' in axis '1'.
```
Also, there is no need to post your logs as we also have access to those.
Hope this helps!
Drop files to upload
My submission (ID: 9714734) has encountered an error during scoring. page is loading…