STDERR: 2021-08-20T18:56:03.023122947Z 3aba68878ed9 2021-08-20 18:56:03,022 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-20T18:56:06.167901304Z 3aba68878ed9 2021-08-20 18:56:06,167 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2021-08-20T18:56:06.167930818Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-20T18:56:06.167933977Z ["null", "File"] may be
STDERR: 2021-08-20T18:56:06.167936864Z incompatible
STDERR: 2021-08-20T18:56:06.167939630Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:135:9: with sink 'input_file' of
STDERR: 2021-08-20T18:56:06.167942205Z type "File"
STDERR: 2021-08-20T18:56:06.167944811Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-20T18:56:06.167947386Z ["null", "File"] may be
STDERR: 2021-08-20T18:56:06.167949783Z incompatible
STDERR: 2021-08-20T18:56:06.167952365Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:75:9: with sink 'input_file' of
STDERR: 2021-08-20T18:56:06.167954789Z type "File"
STDERR: 2021-08-20T18:56:08.498598014Z 3aba68878ed9 2021-08-20 18:56:08,498 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-20T18:56:09.340556781Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp03qb7v4r/worker_log.txt
STDERR: 2021-08-20T18:56:09.636183535Z 3aba68878ed9 2021-08-20 18:56:09,635 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2021-08-20T18:56:09.636700492Z 3aba68878ed9 2021-08-20 18:56:09,636 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-6a16uu9q with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:56:09.636754473Z 3aba68878ed9 2021-08-20 18:56:09,636 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-0t9vl6jq with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:56:09.636831904Z 3aba68878ed9 2021-08-20 18:56:09,636 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-cno425h_ with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:56:10.518394515Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp7ufy_n8c/worker_log.txt
STDERR: 2021-08-20T18:56:10.532003897Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpf7x4qqo2/worker_log.txt
STDERR: 2021-08-20T18:56:10.569624179Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmponezafrg/worker_log.txt
STDERR: 2021-08-20T18:57:20.920180512Z 3aba68878ed9 2021-08-20 18:57:20,918 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-cno425h_
STDERR: 2021-08-20T18:57:33.193906796Z 3aba68878ed9 2021-08-20 18:57:33,193 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-0t9vl6jq
STDERR: 2021-08-20T18:57:37.294414194Z 3aba68878ed9 2021-08-20 18:57:37,294 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-6a16uu9q
STDERR: 2021-08-20T18:57:37.295123348Z 3aba68878ed9 2021-08-20 18:57:37,294 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_validate.cwl/instance-ch7wcpd_ with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:57:37.994278271Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp2o6cq_y1/worker_log.txt
STDERR: 2021-08-20T18:58:10.923606915Z 3aba68878ed9 2021-08-20 18:58:10,923 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_validate.cwl/instance-ch7wcpd_
STDERR: 2021-08-20T18:58:10.924266492Z 3aba68878ed9 2021-08-20 18:58:10,924 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-m89lws9d with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:58:10.924326601Z 3aba68878ed9 2021-08-20 18:58:10,924 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-ya0n06eo with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:58:11.866141976Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp5zqh2wv6/worker_log.txt
STDERR: 2021-08-20T18:58:11.878686270Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpitlqh_fd/worker_log.txt
STDERR: 2021-08-20T18:59:09.913416030Z 3aba68878ed9 2021-08-20 18:59:09,912 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-ya0n06eo
STDERR: 2021-08-20T18:59:13.691885338Z 3aba68878ed9 2021-08-20 18:59:13,691 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-m89lws9d
STDERR: 2021-08-20T18:59:13.692371401Z 3aba68878ed9 2021-08-20 18:59:13,692 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-4ldgoofe with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:59:14.748157159Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp6iw7xfgj/worker_log.txt
STDERR: 2021-08-20T18:59:15.107307267Z 3aba68878ed9 2021-08-20 18:59:15,106 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-4ldgoofe
STDERR: 2021-08-20T18:59:15.108052391Z 3aba68878ed9 2021-08-20 18:59:15,107 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score.cwl/instance-8o9_glg5 with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T18:59:15.789725929Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmp5fspo6kb/worker_log.txt
STDERR: 2021-08-20T19:00:46.039953472Z 3aba68878ed9 2021-08-20 19:00:46,039 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score.cwl/instance-8o9_glg5
STDERR: 2021-08-20T19:00:46.040475285Z 3aba68878ed9 2021-08-20 19:00:46,040 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score_email.cwl/instance-ztd1f476 with job batch system ID: 9 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T19:00:46.040530798Z 3aba68878ed9 2021-08-20 19:00:46,040 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-hz65dpjv with job batch system ID: 10 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T19:00:46.705352422Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpisszt8ol/worker_log.txt
STDERR: 2021-08-20T19:00:46.839907292Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpeily9nve/worker_log.txt
STDERR: 2021-08-20T19:01:58.789687721Z 3aba68878ed9 2021-08-20 19:01:58,789 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-hz65dpjv
STDERR: 2021-08-20T19:02:07.859573248Z 3aba68878ed9 2021-08-20 19:02:07,859 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score_email.cwl/instance-ztd1f476
STDERR: 2021-08-20T19:02:07.860119047Z 3aba68878ed9 2021-08-20 19:02:07,859 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-vmq32hng with job batch system ID: 11 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-20T19:02:08.612933617Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpznthr1yy/worker_log.txt
STDERR: 2021-08-20T19:02:08.871579165Z 3aba68878ed9 2021-08-20 19:02:08,871 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-vmq32hng
STDERR: 2021-08-20T19:02:08.871980877Z 3aba68878ed9 2021-08-20 19:02:08,871 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-vmq32hng
STDERR: 2021-08-20T19:02:08.872109504Z 3aba68878ed9 2021-08-20 19:02:08,872 MainThread WARNING toil.leader: Log from job kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-vmq32hng follows:
STDERR: 2021-08-20T19:02:08.872116776Z =========>
STDERR: 2021-08-20T19:02:08.872120198Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2021-08-20T19:02:08.872123229Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-20T19:02:08.872126254Z Failed to evaluate expression:
STDERR: 2021-08-20T19:02:08.872129071Z Expression evaluation error:
STDERR: 2021-08-20T19:02:08.872131888Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-20T19:02:08.872134663Z script was:
STDERR: 2021-08-20T19:02:08.872137339Z 01 "use strict";
STDERR: 2021-08-20T19:02:08.872140226Z 02 var inputs = {
STDERR: 2021-08-20T19:02:08.872142910Z 03 "status": "INVALID",
STDERR: 2021-08-20T19:02:08.872145945Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-20T19:02:08.872149065Z 05 "previous_email_finished": true
STDERR: 2021-08-20T19:02:08.872151859Z 06 };
STDERR: 2021-08-20T19:02:08.872154678Z 07 var self = null;
STDERR: 2021-08-20T19:02:08.872157410Z 08 var runtime = {
STDERR: 2021-08-20T19:02:08.872160237Z 09 "cores": 1,
STDERR: 2021-08-20T19:02:08.872162942Z 10 "ram": 100.0,
STDERR: 2021-08-20T19:02:08.872165755Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-20T19:02:08.872168986Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-20T19:02:08.872171785Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/tmpa6fulw8m",
STDERR: 2021-08-20T19:02:08.872174999Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpznthr1yy/133b821b-5934-4764-9238-ae23059faa81/t7wthzac3/tmp-outrxcjxjyv"
STDERR: 2021-08-20T19:02:08.872178786Z 15 };
STDERR: 2021-08-20T19:02:08.872183192Z 16 (function(){
STDERR: 2021-08-20T19:02:08.872186220Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-20T19:02:08.872189205Z 18 throw 'invalid submission';
STDERR: 2021-08-20T19:02:08.872191900Z 19 } else {
STDERR: 2021-08-20T19:02:08.872194694Z 20 return {finished: true};
STDERR: 2021-08-20T19:02:08.872197465Z 21 }
STDERR: 2021-08-20T19:02:08.872200065Z 22 })()
STDERR: 2021-08-20T19:02:08.872202766Z stdout was: ''
STDERR: 2021-08-20T19:02:08.872210180Z stderr was: 'invalid submission'
STDERR: 2021-08-20T19:02:08.872213029Z
STDERR: 2021-08-20T19:02:08.872215640Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2021-08-20T19:02:08.872218455Z Expression evaluation error:
STDERR: 2021-08-20T19:02:08.872221488Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-20T19:02:08.872224380Z script was:
STDERR: 2021-08-20T19:02:08.872227010Z 01 "use strict";
STDERR: 2021-08-20T19:02:08.872229712Z 02 var inputs = {
STDERR: 2021-08-20T19:02:08.872232478Z 03 "status": "INVALID",
STDERR: 2021-08-20T19:02:08.872235298Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-20T19:02:08.872238230Z 05 "previous_email_finished": true
STDERR: 2021-08-20T19:02:08.872241123Z 06 };
STDERR: 2021-08-20T19:02:08.872243698Z 07 var self = null;
STDERR: 2021-08-20T19:02:08.872246320Z 08 var runtime = {
STDERR: 2021-08-20T19:02:08.872248886Z 09 "cores": 1,
STDERR: 2021-08-20T19:02:08.872251685Z 10 "ram": 100.0,
STDERR: 2021-08-20T19:02:08.872254362Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-20T19:02:08.872257056Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-20T19:02:08.872259883Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/tmpa6fulw8m",
STDERR: 2021-08-20T19:02:08.872263494Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpznthr1yy/133b821b-5934-4764-9238-ae23059faa81/t7wthzac3/tmp-outrxcjxjyv"
STDERR: 2021-08-20T19:02:08.872266922Z 15 };
STDERR: 2021-08-20T19:02:08.872269630Z 16 (function(){
STDERR: 2021-08-20T19:02:08.872272288Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-20T19:02:08.872286345Z 18 throw 'invalid submission';
STDERR: 2021-08-20T19:02:08.872289485Z 19 } else {
STDERR: 2021-08-20T19:02:08.872292107Z 20 return {finished: true};
STDERR: 2021-08-20T19:02:08.872294908Z 21 }
STDERR: 2021-08-20T19:02:08.872297516Z 22 })()
STDERR: 2021-08-20T19:02:08.872300086Z stdout was: ''
STDERR: 2021-08-20T19:02:08.872302704Z stderr was: 'invalid submission'
STDERR: 2021-08-20T19:02:08.872305415Z
STDERR: 2021-08-20T19:02:08.872308155Z Traceback (most recent call last):
STDERR: 2021-08-20T19:02:08.872310951Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2021-08-20T19:02:08.872314287Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2021-08-20T19:02:08.872317294Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2021-08-20T19:02:08.872320256Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2021-08-20T19:02:08.872325923Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run
STDERR: 2021-08-20T19:02:08.872329202Z return self.run(fileStore)
STDERR: 2021-08-20T19:02:08.872331950Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2021-08-20T19:02:08.872335012Z raise cwltool.errors.WorkflowException(status)
STDERR: 2021-08-20T19:02:08.872337752Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2021-08-20T19:02:08.872340520Z ERROR:toil.worker:Exiting the worker because of a failed job on host 3aba68878ed9
STDERR: 2021-08-20T19:02:08.872343578Z 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-vmq32hng with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-vmq32hng to 0
STDERR: 2021-08-20T19:02:08.872348018Z <=========
STDERR: 2021-08-20T19:02:08.872354703Z 3aba68878ed9 2021-08-20 19:02:08,872 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-vmq32hng with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-vmq32hng is completely failed
STDERR: 2021-08-20T19:02:26.039548543Z 3aba68878ed9 2021-08-20 19:02:26,039 MainThread INFO toil.leader: Finished toil run with 11 failed jobs.
STDERR: 2021-08-20T19:02:26.039630388Z 3aba68878ed9 2021-08-20 19:02:26,039 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-4ldgoofe 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score_email.cwl/instance-ztd1f476 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_validate.cwl/instance-ch7wcpd_ '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-vmq32hng '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-hz65dpjv '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-m89lws9d '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-6a16uu9q 'CWLWorkflow' kind-CWLWorkflow/instance-ejatbv3a 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score.cwl/instance-8o9_glg5 '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-ya0n06eo '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-cno425h_
STDERR: 2021-08-20T19:02:26.050847858Z Traceback (most recent call last):
STDERR: 2021-08-20T19:02:26.050874188Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2021-08-20T19:02:26.050877885Z sys.exit(main())
STDERR: 2021-08-20T19:02:26.050880509Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2021-08-20T19:02:26.050883520Z outobj = toil.start(wf1)
STDERR: 2021-08-20T19:02:26.050886201Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start
STDERR: 2021-08-20T19:02:26.050890447Z return self._runMainLoop(rootJobGraph)
STDERR: 2021-08-20T19:02:26.050893022Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop
STDERR: 2021-08-20T19:02:26.050895845Z jobCache=self._jobCache).run()
STDERR: 2021-08-20T19:02:26.050898588Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run
STDERR: 2021-08-20T19:02:26.050901374Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2021-08-20T19:02:26.050905652Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/tmp4myyaw__' 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-4ldgoofe, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score_email.cwl/instance-ztd1f476, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_validate.cwl/instance-ch7wcpd_, '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-vmq32hng, '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-hz65dpjv, '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-m89lws9d, '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-6a16uu9q, 'CWLWorkflow' kind-CWLWorkflow/instance-ejatbv3a, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3bf8a211-954d-4c33-91eb-10bd38a9cab7_brats-dream-challenge-infra-main_score.cwl/instance-8o9_glg5, '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-ya0n06eo, '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-cno425h_
STDERR: 2021-08-20T19:02:26.050927191Z 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-vmq32hng follows:
STDERR: 2021-08-20T19:02:26.050930366Z =========>
STDERR: 2021-08-20T19:02:26.050932852Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2021-08-20T19:02:26.050935378Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-20T19:02:26.050938152Z Failed to evaluate expression:
STDERR: 2021-08-20T19:02:26.050940905Z Expression evaluation error:
STDERR: 2021-08-20T19:02:26.050943421Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-20T19:02:26.050945911Z script was:
STDERR: 2021-08-20T19:02:26.050948435Z 01 "use strict";
STDERR: 2021-08-20T19:02:26.050950920Z 02 var inputs = {
STDERR: 2021-08-20T19:02:26.050953408Z 03 "status": "INVALID",
STDERR: 2021-08-20T19:02:26.050955900Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-20T19:02:26.050958531Z 05 "previous_email_finished": true
STDERR: 2021-08-20T19:02:26.050961182Z 06 };
STDERR: 2021-08-20T19:02:26.050963571Z 07 var self = null;
STDERR: 2021-08-20T19:02:26.050965982Z 08 var runtime = {
STDERR: 2021-08-20T19:02:26.050968318Z 09 "cores": 1,
STDERR: 2021-08-20T19:02:26.050970796Z 10 "ram": 100.0,
STDERR: 2021-08-20T19:02:26.050973195Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-20T19:02:26.050975907Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-20T19:02:26.050978427Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/tmpa6fulw8m",
STDERR: 2021-08-20T19:02:26.050983559Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpznthr1yy/133b821b-5934-4764-9238-ae23059faa81/t7wthzac3/tmp-outrxcjxjyv"
STDERR: 2021-08-20T19:02:26.050986756Z 15 };
STDERR: 2021-08-20T19:02:26.050989084Z 16 (function(){
STDERR: 2021-08-20T19:02:26.050991628Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-20T19:02:26.050994188Z 18 throw 'invalid submission';
STDERR: 2021-08-20T19:02:26.050996612Z 19 } else {
STDERR: 2021-08-20T19:02:26.050999037Z 20 return {finished: true};
STDERR: 2021-08-20T19:02:26.051001529Z 21 }
STDERR: 2021-08-20T19:02:26.051003887Z 22 })()
STDERR: 2021-08-20T19:02:26.051006262Z stdout was: ''
STDERR: 2021-08-20T19:02:26.051008669Z stderr was: 'invalid submission'
STDERR: 2021-08-20T19:02:26.051011123Z
STDERR: 2021-08-20T19:02:26.051013448Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2021-08-20T19:02:26.051015900Z Expression evaluation error:
STDERR: 2021-08-20T19:02:26.051018336Z Expecting value: line 1 column 1 (char 0)
STDERR: 2021-08-20T19:02:26.051020800Z script was:
STDERR: 2021-08-20T19:02:26.051023152Z 01 "use strict";
STDERR: 2021-08-20T19:02:26.051025572Z 02 var inputs = {
STDERR: 2021-08-20T19:02:26.051027966Z 03 "status": "INVALID",
STDERR: 2021-08-20T19:02:26.051030446Z 04 "previous_annotation_finished": true,
STDERR: 2021-08-20T19:02:26.051032972Z 05 "previous_email_finished": true
STDERR: 2021-08-20T19:02:26.051035557Z 06 };
STDERR: 2021-08-20T19:02:26.051037871Z 07 var self = null;
STDERR: 2021-08-20T19:02:26.051040230Z 08 var runtime = {
STDERR: 2021-08-20T19:02:26.051042575Z 09 "cores": 1,
STDERR: 2021-08-20T19:02:26.051044990Z 10 "ram": 100.0,
STDERR: 2021-08-20T19:02:26.051047412Z 11 "tmpdirSize": 1024,
STDERR: 2021-08-20T19:02:26.051049914Z 12 "outdirSize": 0.95367431640625,
STDERR: 2021-08-20T19:02:26.051052397Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/tmpa6fulw8m",
STDERR: 2021-08-20T19:02:26.051055260Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3bf8a211-954d-4c33-91eb-10bd38a9cab7/node-7f8bfa2a-953b-46b7-82aa-a245ed5dc070-16349ee66b573b0d6cff3dbc6912349f/tmpznthr1yy/133b821b-5934-4764-9238-ae23059faa81/t7wthzac3/tmp-outrxcjxjyv"
STDERR: 2021-08-20T19:02:26.051058361Z 15 };
STDERR: 2021-08-20T19:02:26.051060651Z 16 (function(){
STDERR: 2021-08-20T19:02:26.051063026Z 17 if(inputs.status == "INVALID"){
STDERR: 2021-08-20T19:02:26.051065600Z 18 throw 'invalid submission';
STDERR: 2021-08-20T19:02:26.051068000Z 19 } else {
STDERR: 2021-08-20T19:02:26.051070472Z 20 return {finished: true};
STDERR: 2021-08-20T19:02:26.051080583Z 21 }
STDERR: 2021-08-20T19:02:26.051082997Z 22 })()
STDERR: 2021-08-20T19:02:26.051085361Z stdout was: ''
STDERR: 2021-08-20T19:02:26.051087761Z stderr was: 'invalid submission'
STDERR: 2021-08-20T19:02:26.051090317Z
STDERR: 2021-08-20T19:02:26.051092887Z Traceback (most recent call last):
STDERR: 2021-08-20T19:02:26.051095313Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2021-08-20T19:02:26.051098033Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2021-08-20T19:02:26.051100626Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2021-08-20T19:02:26.051103266Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2021-08-20T19:02:26.051105779Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run
STDERR: 2021-08-20T19:02:26.051108348Z return self.run(fileStore)
STDERR: 2021-08-20T19:02:26.051110793Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2021-08-20T19:02:26.051113395Z raise cwltool.errors.WorkflowException(status)
STDERR: 2021-08-20T19:02:26.051115826Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2021-08-20T19:02:26.051118411Z ERROR:toil.worker:Exiting the worker because of a failed job on host 3aba68878ed9
STDERR: 2021-08-20T19:02:26.051121034Z 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-vmq32hng with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-vmq32hng to 0
STDERR: 2021-08-20T19:02:26.051124610Z <=========
The submitted file : https://www.synapse.org/#!Synapse:syn26118296/files/
Created by Emirhan Kurtulu? ekurtulus Dear @ekurtulus and team,
Submission 9714983 cannot be properly scored due to a size mismatch between your predictions and the references:
```
Size mismatch at dimension '0'
```
Also, you do not need to post your logs on the discussion board as we will also have access to those.
Hope this helps!
Drop files to upload
INVALID SUBMISSION SUBMISSION ID: 9714983 page is loading…