STDERR: 2019-10-29T18:51:01.108478968Z sys.exit(main()) STDERR: 2019-10-29T18:51:01.108484819Z File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main STDERR: 2019-10-29T18:51:01.108665879Z outobj = toil.start(wf1) STDERR: 2019-10-29T18:51:01.108678409Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 781, in start STDERR: 2019-10-29T18:51:01.108895480Z return self._runMainLoop(rootJobGraph) STDERR: 2019-10-29T18:51:01.108907190Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop STDERR: 2019-10-29T18:51:01.109163141Z jobCache=self._jobCache).run() STDERR: 2019-10-29T18:51:01.109170792Z File "/usr/local/lib/python2.7/site-packages/toil/leader.py", line 246, in run STDERR: 2019-10-29T18:51:01.109241112Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-10-29T18:51:01.109253481Z toil.leader.FailedJobsException" />

Hi, my submission is failing the fast lane test and I am a bit at a loss as to why. The training phase completes fine but it fails before/when running the infer.sh. I paste below the log file. My only guess is that I might be running over /scratch allocated disk space but this is unclear (the script generate roughly 4Go files) . Thie script runs fine locally and within the hour mark. I'd appreciate any pointers on what's happening. Cheers, Thomas STDERR: 2019-10-29T18:20:55.934706198Z INFO:cwltool:Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/main_docker_agent_workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/main_docker_agent_workflow.cwl' STDERR: 2019-10-29T18:20:58.204531308Z EHR-challenge-develop/main_docker_agent_workflow.cwl:143:9: object id `EHR-challenge-develop/main_docker_agent_workflow.cwl#run_docker_infer/status` previously defined STDERR: 2019-10-29T18:20:58.204560469Z WARNING:salad:EHR-challenge-develop/main_docker_agent_workflow.cwl:143:9: object id `EHR-challenge-develop/main_docker_agent_workflow.cwl#run_docker_infer/status` previously defined STDERR: 2019-10-29T18:20:58.206042716Z EHR-challenge-develop/main_docker_agent_workflow.cwl:117:9: object id `EHR-challenge-develop/main_docker_agent_workflow.cwl#run_docker_train/status` previously defined STDERR: 2019-10-29T18:20:58.206055807Z WARNING:salad:EHR-challenge-develop/main_docker_agent_workflow.cwl:117:9: object id `EHR-challenge-develop/main_docker_agent_workflow.cwl#run_docker_train/status` previously defined STDERR: 2019-10-29T18:21:02.308022575Z EHR-challenge-develop/run_synthetic_infer_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_infer_docker.cwl#status` previously defined STDERR: 2019-10-29T18:21:02.308054706Z WARNING:salad:EHR-challenge-develop/run_synthetic_infer_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_infer_docker.cwl#status` previously defined STDERR: 2019-10-29T18:21:02.548290816Z EHR-challenge-develop/run_synthetic_training_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_training_docker.cwl#status` previously defined STDERR: 2019-10-29T18:21:02.548312857Z WARNING:salad:EHR-challenge-develop/run_synthetic_training_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_training_docker.cwl#status` previously defined STDERR: 2019-10-29T18:21:03.685598378Z WARNING:toil.batchSystems.singleMachine:Limiting maxCores to CPU count of system (32). STDERR: 2019-10-29T18:21:03.685617118Z WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (268108005376). STDERR: 2019-10-29T18:21:03.685778989Z WARNING:toil.batchSystems.singleMachine:Limiting maxDisk to physically available disk (298789081088). STDERR: 2019-10-29T18:21:03.892040563Z INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. STDERR: 2019-10-29T18:21:04.181954370Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:04.183016925Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpE0XnGx/worker_log.txt STDERR: 2019-10-29T18:21:05.021021339Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python d/P/job1BIlwx with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:05.028208847Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python q/a/jobqJMw3V with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:05.029306742Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python 5/4/jobeWGsjf with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:05.030068946Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python d/O/joboVpppZ with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:05.323665721Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:05.324845096Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpFoA3sB/worker_log.txt STDERR: 2019-10-29T18:21:05.344164836Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:05.345381123Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpzJuRmk/worker_log.txt STDERR: 2019-10-29T18:21:05.357663615Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:05.358960832Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpd3MuLu/worker_log.txt STDERR: 2019-10-29T18:21:05.376180921Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:05.377333778Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpVWvkhd/worker_log.txt STDERR: 2019-10-29T18:21:07.146026958Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python 5/4/jobeWGsjf STDERR: 2019-10-29T18:21:07.661590596Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python q/a/jobqJMw3V STDERR: 2019-10-29T18:21:07.876275863Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python d/P/job1BIlwx STDERR: 2019-10-29T18:21:07.877639980Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python l/M/jobSyqd2Y with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:08.180464211Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:08.181712627Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpgygVMN/worker_log.txt STDERR: 2019-10-29T18:21:08.249777308Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python d/O/joboVpppZ STDERR: 2019-10-29T18:21:10.965941370Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python l/M/jobSyqd2Y STDERR: 2019-10-29T18:21:10.966836065Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/annotate_submission.cwl' python 3/4/jobl7aYpf with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:10.967126156Z INFO:toil.leader:Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p with job batch system ID: 7 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-29T18:21:11.262237986Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:11.263182701Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpzrLjTb/worker_log.txt STDERR: 2019-10-29T18:21:11.273876876Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd'. STDERR: 2019-10-29T18:21:11.274796161Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/toil-9509264a-b469-4393-bc72-39debb91603b-3bdead962f93fd7fa17dcb3c0b3ee830/tmpKc6RgO/worker_log.txt STDERR: 2019-10-29T18:21:14.135297301Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/annotate_submission.cwl' python 3/4/jobl7aYpf STDERR: 2019-10-29T18:50:51.648332792Z INFO:toil.leader:Job ended successfully: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p STDERR: 2019-10-29T18:50:51.648658544Z WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p STDERR: 2019-10-29T18:50:51.648709074Z WARNING:toil.leader:V/U/jobIQVz2p 3a8eaf", STDERR: 2019-10-29T18:50:51.648807254Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99818", STDERR: 2019-10-29T18:50:51.648820485Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.648989905Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99818", STDERR: 2019-10-29T18:50:51.649028866Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99818", STDERR: 2019-10-29T18:50:51.649428896Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.649442887Z WARNING:toil.leader:V/U/jobIQVz2p "size": 1097 STDERR: 2019-10-29T18:50:51.649446907Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.649450237Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.649453857Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$77480052c8a1ef6ab4fe1b7872b16ccadde44b29", STDERR: 2019-10-29T18:50:51.649457427Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99819", STDERR: 2019-10-29T18:50:51.649460837Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.649464017Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99819", STDERR: 2019-10-29T18:50:51.649467477Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99819", STDERR: 2019-10-29T18:50:51.649536797Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.649545828Z WARNING:toil.leader:V/U/jobIQVz2p "size": 392 STDERR: 2019-10-29T18:50:51.649618538Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.649626478Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.649753659Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$31cdf3049b2925ad88ccebce3172ef4c1cef982c", STDERR: 2019-10-29T18:50:51.649762109Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99820", STDERR: 2019-10-29T18:50:51.649842778Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.649861459Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99820", STDERR: 2019-10-29T18:50:51.649984819Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99820", STDERR: 2019-10-29T18:50:51.649993699Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.650097759Z WARNING:toil.leader:V/U/jobIQVz2p "size": 251 STDERR: 2019-10-29T18:50:51.650112650Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.650195310Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.650206070Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$beae8c9a785e4127c24f72d295b7ab6221a9ab2a", STDERR: 2019-10-29T18:50:51.650308220Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99822", STDERR: 2019-10-29T18:50:51.650320840Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.650415431Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99822", STDERR: 2019-10-29T18:50:51.650434351Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99822", STDERR: 2019-10-29T18:50:51.650526222Z WARNING:toil.leader:V/U/jobIQVz2p "class": 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2019-10-29T18:50:51.710474042Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.710575642Z WARNING:toil.leader:V/U/jobIQVz2p "size": 5630 STDERR: 2019-10-29T18:50:51.710581882Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.710707552Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.710720042Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$50ca1c123f8199e8d806fadc2037c07d032f5d90", STDERR: 2019-10-29T18:50:51.710830603Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99998", STDERR: 2019-10-29T18:50:51.710838113Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.710908813Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99998", STDERR: 2019-10-29T18:50:51.710921234Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99998", STDERR: 2019-10-29T18:50:51.711036223Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.711042693Z WARNING:toil.leader:V/U/jobIQVz2p "size": 839 STDERR: 2019-10-29T18:50:51.711111674Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.711120854Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.711269265Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$64bbd2fa569946e6febb2662531cb5196af90390", STDERR: 2019-10-29T18:50:51.711276275Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_patient_99999", STDERR: 2019-10-29T18:50:51.711326355Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.711342135Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_patient_99999", STDERR: 2019-10-29T18:50:51.711437575Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_patient_99999", STDERR: 2019-10-29T18:50:51.711445775Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.711535006Z WARNING:toil.leader:V/U/jobIQVz2p "size": 731 STDERR: 2019-10-29T18:50:51.711545595Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.711611736Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.711617836Z WARNING:toil.leader:V/U/jobIQVz2p "class": "Directory", STDERR: 2019-10-29T18:50:51.711716156Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "train_processed", STDERR: 2019-10-29T18:50:51.711725307Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/scratch/train_processed", STDERR: 2019-10-29T18:50:51.711804067Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": "", STDERR: 2019-10-29T18:50:51.711810307Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "train_processed" STDERR: 2019-10-29T18:50:51.711890477Z WARNING:toil.leader:V/U/jobIQVz2p } STDERR: 2019-10-29T18:50:51.711898807Z WARNING:toil.leader:V/U/jobIQVz2p ], STDERR: 2019-10-29T18:50:51.711973528Z WARNING:toil.leader:V/U/jobIQVz2p "model": [ STDERR: 2019-10-29T18:50:51.712042968Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.712050378Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$2f82104e66ed3a43ca3ac0a9bf37a3e765acc749", STDERR: 2019-10-29T18:50:51.712057758Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_0.pt", STDERR: 2019-10-29T18:50:51.712142658Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.712155318Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_0", STDERR: 2019-10-29T18:50:51.712273389Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_0.pt", STDERR: 2019-10-29T18:50:51.712281319Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.712361609Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.712368149Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.712424479Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.712432079Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$237448d818b39bac794d7269e8e056ff444704f0", STDERR: 2019-10-29T18:50:51.712539610Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_1.pt", STDERR: 2019-10-29T18:50:51.712545360Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.712625030Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_1", STDERR: 2019-10-29T18:50:51.712636910Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_1.pt", STDERR: 2019-10-29T18:50:51.712716360Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.712722631Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.712811131Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.712820041Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.712888851Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$a935d83f6eef354779d3fe5324a66e21b7145a95", STDERR: 2019-10-29T18:50:51.712957611Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_2.pt", STDERR: 2019-10-29T18:50:51.712966151Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.712970242Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_2", STDERR: 2019-10-29T18:50:51.713058232Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_2.pt", STDERR: 2019-10-29T18:50:51.713065322Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.713155122Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.713162043Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.713240303Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.713246703Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$9fa454c34865fe70e1a6d4f5f502e6d9738b34c5", STDERR: 2019-10-29T18:50:51.713330114Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_3.pt", STDERR: 2019-10-29T18:50:51.713344043Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.713409644Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_3", STDERR: 2019-10-29T18:50:51.713479184Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_3.pt", STDERR: 2019-10-29T18:50:51.713492054Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.713540204Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.713564174Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.713638905Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.713698374Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$73ff171859ee2c0675269bec7a145820ff89a3a9", STDERR: 2019-10-29T18:50:51.713704515Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_4.pt", STDERR: 2019-10-29T18:50:51.713755735Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.713819335Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_4", STDERR: 2019-10-29T18:50:51.713828515Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_4.pt", STDERR: 2019-10-29T18:50:51.713860035Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.713923235Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.713932526Z WARNING:toil.leader:V/U/jobIQVz2p }, STDERR: 2019-10-29T18:50:51.714019646Z WARNING:toil.leader:V/U/jobIQVz2p { STDERR: 2019-10-29T18:50:51.714028656Z WARNING:toil.leader:V/U/jobIQVz2p "checksum": "sha1$0e3e3705a22222b561ddf1f64df5d1431568c969", STDERR: 2019-10-29T18:50:51.714120836Z WARNING:toil.leader:V/U/jobIQVz2p "basename": "model_5.pt", STDERR: 2019-10-29T18:50:51.714127107Z WARNING:toil.leader:V/U/jobIQVz2p "nameext": ".pt", STDERR: 2019-10-29T18:50:51.714187557Z WARNING:toil.leader:V/U/jobIQVz2p "nameroot": "model_5", STDERR: 2019-10-29T18:50:51.714195457Z WARNING:toil.leader:V/U/jobIQVz2p "location": "file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/tmpVjsdxd/4/b/out_tmpdirEeqLSs/model/model_5.pt", STDERR: 2019-10-29T18:50:51.714281487Z WARNING:toil.leader:V/U/jobIQVz2p "class": "File", STDERR: 2019-10-29T18:50:51.714289837Z WARNING:toil.leader:V/U/jobIQVz2p "size": 4065213 STDERR: 2019-10-29T18:50:51.714371718Z WARNING:toil.leader:V/U/jobIQVz2p } STDERR: 2019-10-29T18:50:51.714377767Z WARNING:toil.leader:V/U/jobIQVz2p ] STDERR: 2019-10-29T18:50:51.714463257Z WARNING:toil.leader:V/U/jobIQVz2p } STDERR: 2019-10-29T18:50:51.714501558Z WARNING:toil.leader:V/U/jobIQVz2p [job run_synthetic_training_docker.cwl] completed permanentFail STDERR: 2019-10-29T18:50:51.714556238Z WARNING:toil.leader:V/U/jobIQVz2p WARNING:cwltool:[job run_synthetic_training_docker.cwl] completed permanentFail STDERR: 2019-10-29T18:50:51.714563138Z WARNING:toil.leader:V/U/jobIQVz2p Traceback (most recent call last): STDERR: 2019-10-29T18:50:51.714667809Z WARNING:toil.leader:V/U/jobIQVz2p File "/usr/local/lib/python2.7/site-packages/toil/worker.py", line 331, in workerScript STDERR: 2019-10-29T18:50:51.714675769Z WARNING:toil.leader:V/U/jobIQVz2p job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) STDERR: 2019-10-29T18:50:51.714749729Z WARNING:toil.leader:V/U/jobIQVz2p File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1378, in _runner STDERR: 2019-10-29T18:50:51.714757519Z WARNING:toil.leader:V/U/jobIQVz2p returnValues = self._run(jobGraph, fileStore) STDERR: 2019-10-29T18:50:51.714843230Z WARNING:toil.leader:V/U/jobIQVz2p File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1323, in _run STDERR: 2019-10-29T18:50:51.714850360Z WARNING:toil.leader:V/U/jobIQVz2p return self.run(fileStore) STDERR: 2019-10-29T18:50:51.714932060Z WARNING:toil.leader:V/U/jobIQVz2p File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 606, in run STDERR: 2019-10-29T18:50:51.714938710Z WARNING:toil.leader:V/U/jobIQVz2p raise cwltool.errors.WorkflowException(status) STDERR: 2019-10-29T18:50:51.715006310Z WARNING:toil.leader:V/U/jobIQVz2p WorkflowException: permanentFail STDERR: 2019-10-29T18:50:51.715048480Z WARNING:toil.leader:V/U/jobIQVz2p ERROR:toil.worker:Exiting the worker because of a failed job on host a91957eac107 STDERR: 2019-10-29T18:50:51.715120811Z WARNING:toil.leader:V/U/jobIQVz2p WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p with ID V/U/jobIQVz2p to 0 STDERR: 2019-10-29T18:50:51.716561146Z WARNING:toil.leader:Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p with ID V/U/jobIQVz2p is completely failed STDERR: 2019-10-29T18:51:01.027104932Z INFO:toil.leader:Finished toil run with 6 failed jobs. STDERR: 2019-10-29T18:51:01.027236782Z INFO:toil.leader:Failed jobs at end of the run: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python 5/4/jobeWGsjf 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python l/M/jobSyqd2Y 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python d/P/job1BIlwx 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python q/a/jobqJMw3V 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/41b8f4c3-7c8f-4cb6-b83d-82c7d443ee7b/EHR-challenge-develop/run_synthetic_training_docker.cwl' python V/U/jobIQVz2p 'CWLWorkflow' d/p/jobEkoG5u STDERR: 2019-10-29T18:51:01.108427958Z Traceback (most recent call last): STDERR: 2019-10-29T18:51:01.108458338Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2019-10-29T18:51:01.108478968Z sys.exit(main()) STDERR: 2019-10-29T18:51:01.108484819Z File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main STDERR: 2019-10-29T18:51:01.108665879Z outobj = toil.start(wf1) STDERR: 2019-10-29T18:51:01.108678409Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 781, in start STDERR: 2019-10-29T18:51:01.108895480Z return self._runMainLoop(rootJobGraph) STDERR: 2019-10-29T18:51:01.108907190Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop STDERR: 2019-10-29T18:51:01.109163141Z jobCache=self._jobCache).run() STDERR: 2019-10-29T18:51:01.109170792Z File "/usr/local/lib/python2.7/site-packages/toil/leader.py", line 246, in run STDERR: 2019-10-29T18:51:01.109241112Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-10-29T18:51:01.109253481Z toil.leader.FailedJobsException

Created by tgaudelet
Ok, thanks a lot @trberg !
Hi @tgaudelet, It looks like your script is writing directories to the scratch and model folders. Our workflow pipeline is erroring out when it sees new directories in either of those folders. If you only output files into scratch and model, that should solve your problem. Let us know if that doesn't work, Tim
Hi @tgaudelet We are looking into this Tim

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