STDERR: 2019-10-07T21:24:01.028941217Z sys.exit(main()) STDERR: 2019-10-07T21:24:01.028944576Z File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main STDERR: 2019-10-07T21:24:01.029140387Z outobj = toil.start(wf1) STDERR: 2019-10-07T21:24:01.029153338Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 781, in start STDERR: 2019-10-07T21:24:01.029359568Z return self._runMainLoop(rootJobGraph) STDERR: 2019-10-07T21:24:01.029366779Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop STDERR: 2019-10-07T21:24:01.029638990Z jobCache=self._jobCache).run() STDERR: 2019-10-07T21:24:01.029646440Z File "/usr/local/lib/python2.7/site-packages/toil/leader.py", line 246, in run STDERR: 2019-10-07T21:24:01.029692720Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-10-07T21:24:01.029699840Z toil.leader.FailedJobsException" />

Hello, I am submitting this docker image: https://www.synapse.org/#!Synapse:syn20833371/docker/, and receive the below logs. It seems the runDocker.py is receiving the wrong parameter format? here: "STDERR: 2019-10-07T21:23:49.600646835Z WARNING:toil.leader:6/l/jobZ_mLRh runDocker.py: error: argument -f/--scratch_files: expected at least one argument" Thank you for any guidance you can provide. STDERR: 2019-10-07T21:21:17.892890294Z INFO:cwltool:Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/synthetic_docker_agent_workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/synthetic_docker_agent_workflow.cwl' STDERR: 2019-10-07T21:21:19.983037412Z EHR-challenge-develop/synthetic_docker_agent_workflow.cwl:143:9: object id `EHR-challenge-develop/synthetic_docker_agent_workflow.cwl#run_docker_infer/status` previously defined STDERR: 2019-10-07T21:21:19.983065753Z WARNING:salad:EHR-challenge-develop/synthetic_docker_agent_workflow.cwl:143:9: object id `EHR-challenge-develop/synthetic_docker_agent_workflow.cwl#run_docker_infer/status` previously defined STDERR: 2019-10-07T21:21:19.984536810Z EHR-challenge-develop/synthetic_docker_agent_workflow.cwl:117:9: object id `EHR-challenge-develop/synthetic_docker_agent_workflow.cwl#run_docker_train/status` previously defined STDERR: 2019-10-07T21:21:19.984554460Z WARNING:salad:EHR-challenge-develop/synthetic_docker_agent_workflow.cwl:117:9: object id `EHR-challenge-develop/synthetic_docker_agent_workflow.cwl#run_docker_train/status` previously defined STDERR: 2019-10-07T21:21:24.172920914Z EHR-challenge-develop/run_synthetic_infer_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_infer_docker.cwl#status` previously defined STDERR: 2019-10-07T21:21:24.172948914Z 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: 2019-10-07T21:21:24.413721559Z EHR-challenge-develop/run_synthetic_training_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_training_docker.cwl#status` previously defined STDERR: 2019-10-07T21:21:24.413750670Z 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: 2019-10-07T21:21:25.431143130Z WARNING:toil.batchSystems.singleMachine:Limiting maxCores to CPU count of system (32). STDERR: 2019-10-07T21:21:25.431164979Z WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (268107968512). STDERR: 2019-10-07T21:21:25.431298080Z WARNING:toil.batchSystems.singleMachine:Limiting maxDisk to physically available disk (348890705920). STDERR: 2019-10-07T21:21:25.682568574Z INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. STDERR: 2019-10-07T21:21:26.129117970Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:26.130207946Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpMW_diD/worker_log.txt STDERR: 2019-10-07T21:21:26.964320266Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python Z/0/jobWqn294 with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:26.964347346Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python K/O/jobmd6IPZ with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:26.972621335Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python W/f/jobiI969R with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:26.973665610Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python K/c/job0jsCCl with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:27.408865004Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:27.409936089Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpjzpvio/worker_log.txt STDERR: 2019-10-07T21:21:27.422972689Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:27.424071564Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmp7MUt6b/worker_log.txt STDERR: 2019-10-07T21:21:27.424089054Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:27.425327900Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmppqrxzY/worker_log.txt STDERR: 2019-10-07T21:21:27.439709267Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:27.441208593Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpALCsgU/worker_log.txt STDERR: 2019-10-07T21:21:29.239801928Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python K/O/jobmd6IPZ STDERR: 2019-10-07T21:21:29.806263189Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python W/f/jobiI969R STDERR: 2019-10-07T21:21:30.121168546Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python Z/0/jobWqn294 STDERR: 2019-10-07T21:21:30.121917670Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python 2/Z/jobuEoawP with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:30.242580747Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python K/c/job0jsCCl STDERR: 2019-10-07T21:21:30.578182561Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:30.579225575Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpeP1QXT/worker_log.txt STDERR: 2019-10-07T21:21:33.310182789Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python 2/Z/jobuEoawP STDERR: 2019-10-07T21:21:33.311269414Z INFO:toil.leader:Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_training_docker.cwl' python j/k/jobCqWrqk with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:33.318290058Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/annotate_submission.cwl' python T/T/job7bj2eV with job batch system ID: 7 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:21:33.745781874Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:33.746907490Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpmpUpgc/worker_log.txt STDERR: 2019-10-07T21:21:33.752022473Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:21:33.753365640Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpdEFjje/worker_log.txt STDERR: 2019-10-07T21:21:36.485930418Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/annotate_submission.cwl' python T/T/job7bj2eV STDERR: 2019-10-07T21:23:48.120537005Z INFO:toil.leader:Job ended successfully: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_training_docker.cwl' python j/k/jobCqWrqk STDERR: 2019-10-07T21:23:48.121232507Z INFO:toil.leader:Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh with job batch system ID: 8 and cores: 1, disk: 2.0 G, and memory: 100.0 M STDERR: 2019-10-07T21:23:48.552087048Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW'. STDERR: 2019-10-07T21:23:48.552827762Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/toil-d6e49b2a-4ec6-4e61-99e5-5c2bd3fff25c-e89ed93837262f1d6b20cd9e97e84170/tmpuDCzs_/worker_log.txt STDERR: 2019-10-07T21:23:49.596287505Z INFO:toil.leader:Job ended successfully: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh STDERR: 2019-10-07T21:23:49.596869987Z WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh STDERR: 2019-10-07T21:23:49.596995298Z WARNING:toil.leader:6/l/jobZ_mLRh INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2019-10-07T21:23:49.597007568Z WARNING:toil.leader:6/l/jobZ_mLRh INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932. STDERR: 2019-10-07T21:23:49.597162778Z WARNING:toil.leader:6/l/jobZ_mLRh [job run_synthetic_infer_docker.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW/0/6/out_tmpdirA0zHdE$ python \ STDERR: 2019-10-07T21:23:49.597170938Z WARNING:toil.leader:6/l/jobZ_mLRh runDocker.py \ STDERR: 2019-10-07T21:23:49.597305269Z WARNING:toil.leader:6/l/jobZ_mLRh -s \ STDERR: 2019-10-07T21:23:49.597312170Z WARNING:toil.leader:6/l/jobZ_mLRh 9693695 \ STDERR: 2019-10-07T21:23:49.597444680Z WARNING:toil.leader:6/l/jobZ_mLRh -p \ STDERR: 2019-10-07T21:23:49.597451770Z WARNING:toil.leader:6/l/jobZ_mLRh docker.synapse.org/syn20833371/static_person_gradientboost \ STDERR: 2019-10-07T21:23:49.597569350Z WARNING:toil.leader:6/l/jobZ_mLRh -d \ STDERR: 2019-10-07T21:23:49.597628861Z WARNING:toil.leader:6/l/jobZ_mLRh sha256:6c66eb68308d29360261f92f44dfbf80faa7dcc74039f2ef92efed8c8c789c27 \ STDERR: 2019-10-07T21:23:49.597733051Z WARNING:toil.leader:6/l/jobZ_mLRh --status \ STDERR: 2019-10-07T21:23:49.597801261Z WARNING:toil.leader:6/l/jobZ_mLRh VALIDATED \ STDERR: 2019-10-07T21:23:49.597900313Z WARNING:toil.leader:6/l/jobZ_mLRh --parentid \ STDERR: 2019-10-07T21:23:49.597968053Z WARNING:toil.leader:6/l/jobZ_mLRh syn20857827 \ STDERR: 2019-10-07T21:23:49.598064212Z WARNING:toil.leader:6/l/jobZ_mLRh -c \ STDERR: 2019-10-07T21:23:49.598151894Z WARNING:toil.leader:6/l/jobZ_mLRh /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmpmT7G5U/stg8487e962-0b54-4c9d-bd09-b8ad2781bcee/.synapseConfig \ STDERR: 2019-10-07T21:23:49.598227033Z WARNING:toil.leader:6/l/jobZ_mLRh -i \ STDERR: 2019-10-07T21:23:49.598312704Z WARNING:toil.leader:6/l/jobZ_mLRh /home/thomasyu/validation \ STDERR: 2019-10-07T21:23:49.598396635Z WARNING:toil.leader:6/l/jobZ_mLRh -m \ STDERR: 2019-10-07T21:23:49.598500915Z WARNING:toil.leader:6/l/jobZ_mLRh /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmpmT7G5U/stg58ad4c36-ec52-4abf-864a-d17e3693bef8/gb_static_patient_gb.joblib \ STDERR: 2019-10-07T21:23:49.598568576Z WARNING:toil.leader:6/l/jobZ_mLRh -f STDERR: 2019-10-07T21:23:49.598695806Z WARNING:toil.leader:6/l/jobZ_mLRh INFO:cwltool:[job run_synthetic_infer_docker.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmp62FTRW/0/6/out_tmpdirA0zHdE$ python \ STDERR: 2019-10-07T21:23:49.598747326Z WARNING:toil.leader:6/l/jobZ_mLRh runDocker.py \ STDERR: 2019-10-07T21:23:49.598882737Z WARNING:toil.leader:6/l/jobZ_mLRh -s \ STDERR: 2019-10-07T21:23:49.598923207Z WARNING:toil.leader:6/l/jobZ_mLRh 9693695 \ STDERR: 2019-10-07T21:23:49.599043057Z WARNING:toil.leader:6/l/jobZ_mLRh -p \ STDERR: 2019-10-07T21:23:49.599094208Z WARNING:toil.leader:6/l/jobZ_mLRh docker.synapse.org/syn20833371/static_person_gradientboost \ STDERR: 2019-10-07T21:23:49.599198859Z WARNING:toil.leader:6/l/jobZ_mLRh -d \ STDERR: 2019-10-07T21:23:49.599259519Z WARNING:toil.leader:6/l/jobZ_mLRh sha256:6c66eb68308d29360261f92f44dfbf80faa7dcc74039f2ef92efed8c8c789c27 \ STDERR: 2019-10-07T21:23:49.599363179Z WARNING:toil.leader:6/l/jobZ_mLRh --status \ STDERR: 2019-10-07T21:23:49.599422299Z WARNING:toil.leader:6/l/jobZ_mLRh VALIDATED \ STDERR: 2019-10-07T21:23:49.599566460Z WARNING:toil.leader:6/l/jobZ_mLRh --parentid \ STDERR: 2019-10-07T21:23:49.599618850Z WARNING:toil.leader:6/l/jobZ_mLRh syn20857827 \ STDERR: 2019-10-07T21:23:49.599728750Z WARNING:toil.leader:6/l/jobZ_mLRh -c \ STDERR: 2019-10-07T21:23:49.599790461Z WARNING:toil.leader:6/l/jobZ_mLRh /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmpmT7G5U/stg8487e962-0b54-4c9d-bd09-b8ad2781bcee/.synapseConfig \ STDERR: 2019-10-07T21:23:49.599890301Z WARNING:toil.leader:6/l/jobZ_mLRh -i \ STDERR: 2019-10-07T21:23:49.599958242Z WARNING:toil.leader:6/l/jobZ_mLRh /home/thomasyu/validation \ STDERR: 2019-10-07T21:23:49.600057082Z WARNING:toil.leader:6/l/jobZ_mLRh -m \ STDERR: 2019-10-07T21:23:49.600130163Z WARNING:toil.leader:6/l/jobZ_mLRh /var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/tmpmT7G5U/stg58ad4c36-ec52-4abf-864a-d17e3693bef8/gb_static_patient_gb.joblib \ STDERR: 2019-10-07T21:23:49.600212603Z WARNING:toil.leader:6/l/jobZ_mLRh -f STDERR: 2019-10-07T21:23:49.600309863Z WARNING:toil.leader:6/l/jobZ_mLRh usage: runDocker.py [-h] -s SUBMISSIONID -p DOCKER_REPOSITORY -d DOCKER_DIGEST STDERR: 2019-10-07T21:23:49.600388033Z WARNING:toil.leader:6/l/jobZ_mLRh -i INPUT_DIR -c SYNAPSE_CONFIG --parentid PARENTID STDERR: 2019-10-07T21:23:49.600472894Z WARNING:toil.leader:6/l/jobZ_mLRh --status STATUS -m MODEL_FILES [MODEL_FILES ...] -f STDERR: 2019-10-07T21:23:49.600558624Z WARNING:toil.leader:6/l/jobZ_mLRh SCRATCH_FILES [SCRATCH_FILES ...] STDERR: 2019-10-07T21:23:49.600646835Z WARNING:toil.leader:6/l/jobZ_mLRh runDocker.py: error: argument -f/--scratch_files: expected at least one argument STDERR: 2019-10-07T21:23:49.600732465Z WARNING:toil.leader:6/l/jobZ_mLRh Could not collect memory usage, job ended before monitoring began. STDERR: 2019-10-07T21:23:49.600816445Z WARNING:toil.leader:6/l/jobZ_mLRh INFO:cwltool:Could not collect memory usage, job ended before monitoring began. STDERR: 2019-10-07T21:23:49.600914376Z WARNING:toil.leader:6/l/jobZ_mLRh [job run_synthetic_infer_docker.cwl] Job error: STDERR: 2019-10-07T21:23:49.600983077Z WARNING:toil.leader:6/l/jobZ_mLRh Error collecting output for parameter 'predictions': STDERR: 2019-10-07T21:23:49.601080267Z WARNING:toil.leader:6/l/jobZ_mLRh :1:1: Did not find output file with glob pattern: '['output/predictions.csv']' STDERR: 2019-10-07T21:23:49.601153677Z WARNING:toil.leader:6/l/jobZ_mLRh ERROR:cwltool:[job run_synthetic_infer_docker.cwl] Job error: STDERR: 2019-10-07T21:23:49.601260987Z WARNING:toil.leader:6/l/jobZ_mLRh Error collecting output for parameter 'predictions': STDERR: 2019-10-07T21:23:49.601323478Z WARNING:toil.leader:6/l/jobZ_mLRh :1:1: Did not find output file with glob pattern: '['output/predictions.csv']' STDERR: 2019-10-07T21:23:49.601427309Z WARNING:toil.leader:6/l/jobZ_mLRh [job run_synthetic_infer_docker.cwl] completed permanentFail STDERR: 2019-10-07T21:23:49.601497229Z WARNING:toil.leader:6/l/jobZ_mLRh WARNING:cwltool:[job run_synthetic_infer_docker.cwl] completed permanentFail STDERR: 2019-10-07T21:23:49.601583799Z WARNING:toil.leader:6/l/jobZ_mLRh Traceback (most recent call last): STDERR: 2019-10-07T21:23:49.601682110Z WARNING:toil.leader:6/l/jobZ_mLRh File "/usr/local/lib/python2.7/site-packages/toil/worker.py", line 331, in workerScript STDERR: 2019-10-07T21:23:49.601764370Z WARNING:toil.leader:6/l/jobZ_mLRh job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) STDERR: 2019-10-07T21:23:49.601842490Z WARNING:toil.leader:6/l/jobZ_mLRh File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1378, in _runner STDERR: 2019-10-07T21:23:49.601928690Z WARNING:toil.leader:6/l/jobZ_mLRh returnValues = self._run(jobGraph, fileStore) STDERR: 2019-10-07T21:23:49.602221932Z WARNING:toil.leader:6/l/jobZ_mLRh File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1323, in _run STDERR: 2019-10-07T21:23:49.602383703Z WARNING:toil.leader:6/l/jobZ_mLRh return self.run(fileStore) STDERR: 2019-10-07T21:23:49.602437333Z WARNING:toil.leader:6/l/jobZ_mLRh File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 606, in run STDERR: 2019-10-07T21:23:49.602500243Z WARNING:toil.leader:6/l/jobZ_mLRh raise cwltool.errors.WorkflowException(status) STDERR: 2019-10-07T21:23:49.602509433Z WARNING:toil.leader:6/l/jobZ_mLRh WorkflowException: permanentFail STDERR: 2019-10-07T21:23:49.602574514Z WARNING:toil.leader:6/l/jobZ_mLRh ERROR:toil.worker:Exiting the worker because of a failed job on host cfb18955f444 STDERR: 2019-10-07T21:23:49.602658904Z WARNING:toil.leader:6/l/jobZ_mLRh WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh with ID 6/l/jobZ_mLRh to 0 STDERR: 2019-10-07T21:23:49.604131661Z WARNING:toil.leader:Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh with ID 6/l/jobZ_mLRh is completely failed STDERR: 2019-10-07T21:24:00.956694556Z INFO:toil.leader:Finished toil run with 7 failed jobs. STDERR: 2019-10-07T21:24:00.957144989Z INFO:toil.leader:Failed jobs at end of the run: 'CWLWorkflow' B/2/jobSeA6fH 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python K/O/jobmd6IPZ 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_infer_docker.cwl' python 6/l/jobZ_mLRh 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/109f91c5-c0a4-4f18-99f1-899f9b865fdb/EHR-challenge-develop/run_synthetic_training_docker.cwl' python j/k/jobCqWrqk 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/validate_docker.cwl' python 2/Z/jobuEoawP 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python Z/0/jobWqn294 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python W/f/jobiI969R STDERR: 2019-10-07T21:24:01.028909226Z Traceback (most recent call last): STDERR: 2019-10-07T21:24:01.028936616Z File "/usr/local/bin/toil-cwl-runner", line 10, in STDERR: 2019-10-07T21:24:01.028941217Z sys.exit(main()) STDERR: 2019-10-07T21:24:01.028944576Z File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main STDERR: 2019-10-07T21:24:01.029140387Z outobj = toil.start(wf1) STDERR: 2019-10-07T21:24:01.029153338Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 781, in start STDERR: 2019-10-07T21:24:01.029359568Z return self._runMainLoop(rootJobGraph) STDERR: 2019-10-07T21:24:01.029366779Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop STDERR: 2019-10-07T21:24:01.029638990Z jobCache=self._jobCache).run() STDERR: 2019-10-07T21:24:01.029646440Z File "/usr/local/lib/python2.7/site-packages/toil/leader.py", line 246, in run STDERR: 2019-10-07T21:24:01.029692720Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-10-07T21:24:01.029699840Z toil.leader.FailedJobsException

Created by Ivan Brugere ivanbrugere
Dear @ivanbrugere, Thanks for bringing this to our attention. We have resolved the issue. I also noticed that you attempted to submit a Project, please submit a Docker repository instead of a Project. That being said, one of your failed submissions due to the bug you posted above has ran successfully. Best, Tom

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