I just try to submission with auc.csv from original file, but i fail. I followed tutorial of this site, and all steps were passed. But my submission is fail and log message is like below STDERR: 2020-02-17T02:11:00.230990830Z e351554613f3 2020-02-17 02:11:00,230 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl' STDERR: 2020-02-17T02:11:05.310810425Z e351554613f3 2020-02-17 02:11:05,310 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2020-02-17T02:11:05.310844455Z CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl:53:9: Source 'docker_repository' of type STDERR: 2020-02-17T02:11:05.310849173Z ["null", "string"] may be incompatible STDERR: 2020-02-17T02:11:05.310853085Z CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl:136:9: with sink 'docker_repository' of STDERR: 2020-02-17T02:11:05.310856548Z type "string" STDERR: 2020-02-17T02:11:05.310859930Z CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl:54:9: Source 'docker_digest' of type STDERR: 2020-02-17T02:11:05.310863389Z ["null", "string"] may be incompatible STDERR: 2020-02-17T02:11:05.310867081Z CTD2-BeatAML-Challenge-master/docker_workflow_sc2.cwl:138:9: with sink 'docker_digest' of type STDERR: 2020-02-17T02:11:05.310870441Z "string" STDERR: 2020-02-17T02:11:06.655251636Z e351554613f3 2020-02-17 02:11:06,654 MainThread WARNING toil.batchSystems.singleMachine: Limiting maxCores to CPU count of system (8). STDERR: 2020-02-17T02:11:06.655280927Z e351554613f3 2020-02-17 02:11:06,655 MainThread WARNING toil.batchSystems.singleMachine: Limiting maxMemory to physically available memory (33359032320). STDERR: 2020-02-17T02:11:06.655473254Z e351554613f3 2020-02-17 02:11:06,655 MainThread WARNING toil.batchSystems.singleMachine: Limiting maxDisk to physically available disk (199328305152). STDERR: 2020-02-17T02:11:06.703466709Z e351554613f3 2020-02-17 02:11:06,703 MainThread INFO toil: Running Toil version 3.23.1-56ad62624e7d659a7b0fbd7f1e097b880a7833e9. STDERR: 2020-02-17T02:11:07.468723569Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpt4wcvoel/worker_log.txt STDERR: 2020-02-17T02:11:07.792600064Z e351554613f3 2020-02-17 02:11:07,792 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_submission.cwl/instancewa52bh0_ with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:07.796592445Z e351554613f3 2020-02-17 02:11:07,796 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/synapse-client-cwl-tools/v0.1/synapse-get-tool.cwl' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks_synapse-client-cwl-tools_v0.1_synapse-get-tool.cwl/instance05c7zblk with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:07.796765369Z e351554613f3 2020-02-17 02:11:07,796 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/notification_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_notification_email.cwl/instancezvqdm9tq with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:07.796945464Z e351554613f3 2020-02-17 02:11:07,796 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_docker_config.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_docker_config.cwl/instancerwfi7aob with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:08.759985174Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmp6836tu7n/worker_log.txt STDERR: 2020-02-17T02:11:08.893565238Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpqfwqaq6s/worker_log.txt STDERR: 2020-02-17T02:11:08.895538980Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpv30o7v6c/worker_log.txt STDERR: 2020-02-17T02:11:08.944322307Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpehbk97b0/worker_log.txt STDERR: 2020-02-17T02:11:11.264396579Z e351554613f3 2020-02-17 02:11:11,262 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/synapse-client-cwl-tools/v0.1/synapse-get-tool.cwl' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks_synapse-client-cwl-tools_v0.1_synapse-get-tool.cwl/instance05c7zblk STDERR: 2020-02-17T02:11:12.114690437Z e351554613f3 2020-02-17 02:11:12,114 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_docker_config.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_docker_config.cwl/instancerwfi7aob STDERR: 2020-02-17T02:11:12.694985927Z e351554613f3 2020-02-17 02:11:12,694 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/notification_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_notification_email.cwl/instancezvqdm9tq STDERR: 2020-02-17T02:11:13.198354673Z e351554613f3 2020-02-17 02:11:13,198 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_submission.cwl/instancewa52bh0_ STDERR: 2020-02-17T02:11:13.198924282Z e351554613f3 2020-02-17 02:11:13,198 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_docker.cwl/instancep6_iypz5 with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:13.927919993Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpzgbyp2gm/worker_log.txt STDERR: 2020-02-17T02:11:16.461584030Z e351554613f3 2020-02-17 02:11:16,461 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_docker.cwl/instancep6_iypz5 STDERR: 2020-02-17T02:11:16.462353329Z e351554613f3 2020-02-17 02:11:16,462 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_annotate_submission.cwl/instancehgk7qq56 with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:16.467009520Z e351554613f3 2020-02-17 02:11:16,466 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_email.cwl/instancexu3qfdxc with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:16.467117149Z e351554613f3 2020-02-17 02:11:16,467 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:17.238616065Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpy7ik_50j/worker_log.txt STDERR: 2020-02-17T02:11:17.243616602Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpcpx8ckrz/worker_log.txt STDERR: 2020-02-17T02:11:17.268739658Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpeyjl85jb/worker_log.txt STDERR: 2020-02-17T02:11:17.527921518Z e351554613f3 2020-02-17 02:11:17,527 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw STDERR: 2020-02-17T02:11:17.528387688Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw STDERR: 2020-02-17T02:11:17.528454481Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2020-02-17T02:11:17.528517373Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw INFO:toil:Running Toil version 3.23.1-56ad62624e7d659a7b0fbd7f1e097b880a7833e9. STDERR: 2020-02-17T02:11:17.528573083Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw Traceback (most recent call last): STDERR: 2020-02-17T02:11:17.528631709Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/cwltool/process.py", line 382, in fill_in_defaults STDERR: 2020-02-17T02:11:17.528688182Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw raise WorkflowException("Missing required input parameter '%s'" % shortname(inp["id"])) STDERR: 2020-02-17T02:11:17.528748787Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw cwltool.errors.WorkflowException: Missing required input parameter 'docker_repository' STDERR: 2020-02-17T02:11:17.528806309Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw STDERR: 2020-02-17T02:11:17.528862070Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw The above exception was the direct cause of the following exception: STDERR: 2020-02-17T02:11:17.528915845Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw STDERR: 2020-02-17T02:11:17.528975418Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw Traceback (most recent call last): STDERR: 2020-02-17T02:11:17.529023466Z e351554613f3 2020-02-17 02:11:17,528 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2020-02-17T02:11:17.529080327Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2020-02-17T02:11:17.529132202Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2020-02-17T02:11:17.529188943Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw returnValues = self._run(jobGraph, fileStore) STDERR: 2020-02-17T02:11:17.529241180Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2020-02-17T02:11:17.529296837Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw return self.run(fileStore) STDERR: 2020-02-17T02:11:17.529353819Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 574, in run STDERR: 2020-02-17T02:11:17.529410480Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw self.runtime_context.make_fs_access("")) STDERR: 2020-02-17T02:11:17.529456565Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/cwltool/process.py", line 382, in fill_in_defaults STDERR: 2020-02-17T02:11:17.529518465Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw raise WorkflowException("Missing required input parameter '%s'" % shortname(inp["id"])) STDERR: 2020-02-17T02:11:17.529563454Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/schema_salad/sourceline.py", line 324, in __exit__ STDERR: 2020-02-17T02:11:17.529623050Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw raise_from(self.makeError(six.text_type(exc_value)), exc_value) STDERR: 2020-02-17T02:11:17.529676139Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "/usr/local/lib/python3.6/site-packages/future/utils/__init__.py", line 403, in raise_from STDERR: 2020-02-17T02:11:17.529732797Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw exec(execstr, myglobals, mylocals) STDERR: 2020-02-17T02:11:17.529785208Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw File "", line 1, in STDERR: 2020-02-17T02:11:17.529844118Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw cwltool.errors.WorkflowException: CTD2-BeatAML-Challenge-master/run_docker.cwl:12:5: Missing required input parameter 'docker_repository' STDERR: 2020-02-17T02:11:17.529897928Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw ERROR:toil.worker:Exiting the worker because of a failed job on host e351554613f3 STDERR: 2020-02-17T02:11:17.529968583Z e351554613f3 2020-02-17 02:11:17,529 MainThread WARNING toil.leader: kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw to 0 STDERR: 2020-02-17T02:11:17.530936230Z e351554613f3 2020-02-17 02:11:17,530 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw is completely failed STDERR: 2020-02-17T02:11:20.698966630Z e351554613f3 2020-02-17 02:11:20,698 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_annotate_submission.cwl/instancehgk7qq56 STDERR: 2020-02-17T02:11:21.608047131Z e351554613f3 2020-02-17 02:11:21,607 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_email.cwl/instancexu3qfdxc STDERR: 2020-02-17T02:11:21.608590192Z e351554613f3 2020-02-17 02:11:21,608 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz with job batch system ID: 9 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2020-02-17T02:11:22.350687230Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpqqm5t8dc/worker_log.txt STDERR: 2020-02-17T02:11:23.507134189Z e351554613f3 2020-02-17 02:11:23,506 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz STDERR: 2020-02-17T02:11:23.507517938Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz STDERR: 2020-02-17T02:11:23.507588325Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2020-02-17T02:11:23.507597439Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz INFO:toil:Running Toil version 3.23.1-56ad62624e7d659a7b0fbd7f1e097b880a7833e9. STDERR: 2020-02-17T02:11:23.507696895Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Failed to evaluate expression: STDERR: 2020-02-17T02:11:23.507720289Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Expression evaluation error: STDERR: 2020-02-17T02:11:23.507753145Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Expecting value: line 1 column 1 (char 0) STDERR: 2020-02-17T02:11:23.507806934Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz script was: STDERR: 2020-02-17T02:11:23.507864314Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 01 "use strict"; STDERR: 2020-02-17T02:11:23.507904062Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 02 var inputs = { STDERR: 2020-02-17T02:11:23.507944532Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 03 "status": "INVALID", STDERR: 2020-02-17T02:11:23.507988472Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 04 "previous_annotation_finished": true, STDERR: 2020-02-17T02:11:23.508030950Z e351554613f3 2020-02-17 02:11:23,507 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 05 "previous_email_finished": true STDERR: 2020-02-17T02:11:23.508076887Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 06 }; STDERR: 2020-02-17T02:11:23.508131421Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 07 var self = null; STDERR: 2020-02-17T02:11:23.508172545Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 08 var runtime = { STDERR: 2020-02-17T02:11:23.508208503Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 09 "cores": 1, STDERR: 2020-02-17T02:11:23.508264502Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 10 "ram": 100.0, STDERR: 2020-02-17T02:11:23.508315808Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 11 "tmpdirSize": 1024, STDERR: 2020-02-17T02:11:23.508354414Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 12 "outdirSize": 0.95367431640625, STDERR: 2020-02-17T02:11:23.508431282Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/tmp0mw_pibi", STDERR: 2020-02-17T02:11:23.508437993Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpqqm5t8dc/0ba35686-0cee-498e-aaee-9fde9b72bc17/tyxh8bzvv/tmp-outtxs4372q" STDERR: 2020-02-17T02:11:23.508512547Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 15 }; STDERR: 2020-02-17T02:11:23.508553913Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 16 (function(){ STDERR: 2020-02-17T02:11:23.508611280Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 17 if(inputs.status == "INVALID"){ STDERR: 2020-02-17T02:11:23.508719015Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 18 throw 'invalid submission'; STDERR: 2020-02-17T02:11:23.508726035Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 19 } else { STDERR: 2020-02-17T02:11:23.508789961Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 20 return {finished: true}; STDERR: 2020-02-17T02:11:23.508799809Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 21 } STDERR: 2020-02-17T02:11:23.508869859Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 22 })() STDERR: 2020-02-17T02:11:23.508914006Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz stdout was: '' STDERR: 2020-02-17T02:11:23.508982618Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz stderr was: 'invalid submission' STDERR: 2020-02-17T02:11:23.509005817Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz STDERR: 2020-02-17T02:11:23.509070065Z e351554613f3 2020-02-17 02:11:23,508 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz WARNING:cwltool:Failed to evaluate expression: STDERR: 2020-02-17T02:11:23.509114552Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Expression evaluation error: STDERR: 2020-02-17T02:11:23.509175425Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Expecting value: line 1 column 1 (char 0) STDERR: 2020-02-17T02:11:23.509214642Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz script was: STDERR: 2020-02-17T02:11:23.509279560Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 01 "use strict"; STDERR: 2020-02-17T02:11:23.509324091Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 02 var inputs = { STDERR: 2020-02-17T02:11:23.509389586Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 03 "status": "INVALID", STDERR: 2020-02-17T02:11:23.509427046Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 04 "previous_annotation_finished": true, STDERR: 2020-02-17T02:11:23.509503647Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 05 "previous_email_finished": true STDERR: 2020-02-17T02:11:23.509508541Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 06 }; STDERR: 2020-02-17T02:11:23.509563208Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 07 var self = null; STDERR: 2020-02-17T02:11:23.509612297Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 08 var runtime = { STDERR: 2020-02-17T02:11:23.509676417Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 09 "cores": 1, STDERR: 2020-02-17T02:11:23.509680937Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 10 "ram": 100.0, STDERR: 2020-02-17T02:11:23.509751087Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 11 "tmpdirSize": 1024, STDERR: 2020-02-17T02:11:23.509797129Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 12 "outdirSize": 0.95367431640625, STDERR: 2020-02-17T02:11:23.509864547Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/tmp0mw_pibi", STDERR: 2020-02-17T02:11:23.509875405Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/toil-d2c9a43b-72f1-4f53-b530-3bbf6e642aed-04a9330868336aa19c457b402d5a4f7c/tmpqqm5t8dc/0ba35686-0cee-498e-aaee-9fde9b72bc17/tyxh8bzvv/tmp-outtxs4372q" STDERR: 2020-02-17T02:11:23.509942383Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 15 }; STDERR: 2020-02-17T02:11:23.509987861Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 16 (function(){ STDERR: 2020-02-17T02:11:23.510053083Z e351554613f3 2020-02-17 02:11:23,509 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 17 if(inputs.status == "INVALID"){ STDERR: 2020-02-17T02:11:23.510057366Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 18 throw 'invalid submission'; STDERR: 2020-02-17T02:11:23.510127895Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 19 } else { STDERR: 2020-02-17T02:11:23.510174940Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 20 return {finished: true}; STDERR: 2020-02-17T02:11:23.510238157Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 21 } STDERR: 2020-02-17T02:11:23.510242264Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 22 })() STDERR: 2020-02-17T02:11:23.510315131Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz stdout was: '' STDERR: 2020-02-17T02:11:23.510361886Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz stderr was: 'invalid submission' STDERR: 2020-02-17T02:11:23.510449316Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz STDERR: 2020-02-17T02:11:23.510497549Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz Traceback (most recent call last): STDERR: 2020-02-17T02:11:23.510570979Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2020-02-17T02:11:23.510579443Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2020-02-17T02:11:23.510651976Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2020-02-17T02:11:23.510697548Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz returnValues = self._run(jobGraph, fileStore) STDERR: 2020-02-17T02:11:23.510762231Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2020-02-17T02:11:23.510766600Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz return self.run(fileStore) STDERR: 2020-02-17T02:11:23.510837891Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 617, in run STDERR: 2020-02-17T02:11:23.510884325Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz raise cwltool.errors.WorkflowException(status) STDERR: 2020-02-17T02:11:23.510948943Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz cwltool.errors.WorkflowException: permanentFail STDERR: 2020-02-17T02:11:23.510953020Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz ERROR:toil.worker:Exiting the worker because of a failed job on host e351554613f3 STDERR: 2020-02-17T02:11:23.511050119Z e351554613f3 2020-02-17 02:11:23,510 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz to 0 STDERR: 2020-02-17T02:11:23.511277338Z e351554613f3 2020-02-17 02:11:23,511 MainThread WARNING toil.leader: Job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz is completely failed STDERR: 2020-02-17T02:11:34.750971996Z e351554613f3 2020-02-17 02:11:34,750 MainThread INFO toil.leader: Finished toil run with 9 failed jobs. STDERR: 2020-02-17T02:11:34.751031900Z e351554613f3 2020-02-17 02:11:34,750 MainThread INFO toil.leader: Failed jobs at end of the run: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_check_status.cwl/instancecogujvjz 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_email.cwl/instancexu3qfdxc 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_submission.cwl/instancewa52bh0_ 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/get_docker_config.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_get_docker_config.cwl/instancerwfi7aob 'https://raw.githubusercontent.com/Sage-Bionetworks/synapse-client-cwl-tools/v0.1/synapse-get-tool.cwl' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks_synapse-client-cwl-tools_v0.1_synapse-get-tool.cwl/instance05c7zblk 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/validate_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_validate_docker.cwl/instancep6_iypz5 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/3cb3b3ee-a588-4ded-b677-2c26636c29c1/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_3cb3b3ee-a588-4ded-b677-2c26636c29c1_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancelxwdezvw 'CWLWorkflow' kind-CWLWorkflow/instance7khwvcbv 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_annotate_submission.cwl/instancehgk7qq56 STDERR: 2020-02-17T02:11:34.763515557Z Traceback (most recent call last): STDERR: 2020-02-17T02:11:34.763539997Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2020-02-17T02:11:34.763545038Z sys.exit(main()) STDERR: 2020-02-17T02:11:34.763549010Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1357, in main STDERR: 2020-02-17T02:11:34.763552900Z result = toil.start(wf1) STDERR: 2020-02-17T02:11:34.763556630Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 800, in start STDERR: 2020-02-17T02:11:34.763560563Z return self._runMainLoop(rootJobGraph) STDERR: 2020-02-17T02:11:34.763564140Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1070, in _runMainLoop STDERR: 2020-02-17T02:11:34.763567956Z jobCache=self._jobCache).run() STDERR: 2020-02-17T02:11:34.763571284Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 246, in run STDERR: 2020-02-17T02:11:34.763585310Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2020-02-17T02:11:34.763589267Z toil.leader.FailedJobsException