I cloned the example docker and was able to run it locally successfully. However, it failed when i submitted the image and the log file was rather cryptic. I was wondering if anyone successfully submitted a docker image and got a score?
Thanks,
Wendy
Created by Wendy Wong shukwong Great! Good to hear! Hi Tim,
Thanks for looking into the error! You are right! I also discovered that I should have submitted it from the docker repository and it worked fine this time.
Best,
Wendy Hi Wendy,
Are you sure you submitted the docker repository and not the project? The error seems to be "Error collecting output for parameter 'docker_repository'".
This error was thrown in the NCATS cloud environment, which means there was an issue parsing the information between Synapse and NCATS.
Did you submit your model from the docker repository page in Synapse or via the submission button?
Tim Hi Tim ,
I am pasting the log file here. I thought I would ask before trying to output more messages if it's something obvious that I don't see.
Thanks very much for your help!
Wendy
STDERR: 2019-09-28T00:04:12.532081356Z INFO:cwltool:Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/EHR-challenge-develop/synthetic_docker_agent_workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/EHR-challenge-develop/synthetic_docker_agent_workflow.cwl'
STDERR: 2019-09-28T00:04:14.628381084Z 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: 2019-09-28T00:04:14.628409024Z 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: 2019-09-28T00:04:14.629869672Z 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: 2019-09-28T00:04:14.629887332Z 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: 2019-09-28T00:04:18.814709471Z EHR-challenge-develop/run_synthetic_infer_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_infer_docker.cwl#status` previously defined
STDERR: 2019-09-28T00:04:18.814734781Z 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: 2019-09-28T00:04:19.072047957Z EHR-challenge-develop/run_synthetic_training_docker.cwl:22:5: object id `EHR-challenge-develop/run_synthetic_training_docker.cwl#status` previously defined
STDERR: 2019-09-28T00:04:19.072083017Z 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: 2019-09-28T00:04:20.125422032Z WARNING:toil.batchSystems.singleMachine:Limiting maxCores to CPU count of system (32).
STDERR: 2019-09-28T00:04:20.125445093Z WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (268107968512).
STDERR: 2019-09-28T00:04:20.125449542Z WARNING:toil.batchSystems.singleMachine:Limiting maxDisk to physically available disk (414279196672).
STDERR: 2019-09-28T00:04:20.354070557Z INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932.
STDERR: 2019-09-28T00:04:20.777606669Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR'.
STDERR: 2019-09-28T00:04:20.778580605Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/toil-375e6650-cb48-4c91-9b5a-6766f3fa0ced-e89ed93837262f1d6b20cd9e97e84170/tmpA_2c7R/worker_log.txt
STDERR: 2019-09-28T00:04:21.583000076Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python p/G/jobcZamrh with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2019-09-28T00:04:21.589500390Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2019-09-28T00:04:21.590082803Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python s/T/job6Vv4HQ with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2019-09-28T00:04:21.590620686Z INFO:toil.leader:Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python L/l/jobAhrort with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 100.0 M
STDERR: 2019-09-28T00:04:22.097908675Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR'.
STDERR: 2019-09-28T00:04:22.099158412Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/toil-375e6650-cb48-4c91-9b5a-6766f3fa0ced-e89ed93837262f1d6b20cd9e97e84170/tmpxVJLPb/worker_log.txt
STDERR: 2019-09-28T00:04:22.114004639Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR'.
STDERR: 2019-09-28T00:04:22.115227475Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/toil-375e6650-cb48-4c91-9b5a-6766f3fa0ced-e89ed93837262f1d6b20cd9e97e84170/tmpmRqFhR/worker_log.txt
STDERR: 2019-09-28T00:04:22.153855927Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR'.
STDERR: 2019-09-28T00:04:22.155188505Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/toil-375e6650-cb48-4c91-9b5a-6766f3fa0ced-e89ed93837262f1d6b20cd9e97e84170/tmpj1Y1wl/worker_log.txt
STDERR: 2019-09-28T00:04:22.184619608Z DEBUG:toil.jobStores.fileJobStore:Path to job store directory is '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR'.
STDERR: 2019-09-28T00:04:22.185940485Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/toil-375e6650-cb48-4c91-9b5a-6766f3fa0ced-e89ed93837262f1d6b20cd9e97e84170/tmptpi3V3/worker_log.txt
STDERR: 2019-09-28T00:04:24.108610539Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python s/T/job6Vv4HQ
STDERR: 2019-09-28T00:04:24.924649405Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python L/l/jobAhrort
STDERR: 2019-09-28T00:04:25.039260943Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl
STDERR: 2019-09-28T00:04:25.039687525Z WARNING:toil.leader:The job seems to have left a log file, indicating failure: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl
STDERR: 2019-09-28T00:04:25.039791146Z WARNING:toil.leader:9/w/jobwmLNvl INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2019-09-28T00:04:25.039897266Z WARNING:toil.leader:9/w/jobwmLNvl INFO:toil:Running Toil version 3.20.0-cf34ca3416697f2abc816b2538f20ee29ba16932.
STDERR: 2019-09-28T00:04:25.040005407Z WARNING:toil.leader:9/w/jobwmLNvl [job get_submission_docker.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR/8/0/out_tmpdirD1anbF$ python \
STDERR: 2019-09-28T00:04:25.040076418Z WARNING:toil.leader:9/w/jobwmLNvl get_submission_docker.py \
STDERR: 2019-09-28T00:04:25.040187718Z WARNING:toil.leader:9/w/jobwmLNvl -s \
STDERR: 2019-09-28T00:04:25.040248348Z WARNING:toil.leader:9/w/jobwmLNvl 9693305 \
STDERR: 2019-09-28T00:04:25.040342979Z WARNING:toil.leader:9/w/jobwmLNvl -r \
STDERR: 2019-09-28T00:04:25.040419419Z WARNING:toil.leader:9/w/jobwmLNvl results.json \
STDERR: 2019-09-28T00:04:25.040531109Z WARNING:toil.leader:9/w/jobwmLNvl -c \
STDERR: 2019-09-28T00:04:25.040602330Z WARNING:toil.leader:9/w/jobwmLNvl /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8/.synapseConfig
STDERR: 2019-09-28T00:04:25.040738221Z WARNING:toil.leader:9/w/jobwmLNvl INFO:cwltool:[job get_submission_docker.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR/8/0/out_tmpdirD1anbF$ python \
STDERR: 2019-09-28T00:04:25.040783260Z WARNING:toil.leader:9/w/jobwmLNvl get_submission_docker.py \
STDERR: 2019-09-28T00:04:25.040896561Z WARNING:toil.leader:9/w/jobwmLNvl -s \
STDERR: 2019-09-28T00:04:25.040956341Z WARNING:toil.leader:9/w/jobwmLNvl 9693305 \
STDERR: 2019-09-28T00:04:25.041068952Z WARNING:toil.leader:9/w/jobwmLNvl -r \
STDERR: 2019-09-28T00:04:25.041123763Z WARNING:toil.leader:9/w/jobwmLNvl results.json \
STDERR: 2019-09-28T00:04:25.041234503Z WARNING:toil.leader:9/w/jobwmLNvl -c \
STDERR: 2019-09-28T00:04:25.041300854Z WARNING:toil.leader:9/w/jobwmLNvl /var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8/.synapseConfig
STDERR: 2019-09-28T00:04:25.041408884Z WARNING:toil.leader:9/w/jobwmLNvl Welcome, ehrdreamservice!
STDERR: 2019-09-28T00:04:25.041471315Z WARNING:toil.leader:9/w/jobwmLNvl
STDERR: 2019-09-28T00:04:25.041567425Z WARNING:toil.leader:9/w/jobwmLNvl Traceback (most recent call last):
STDERR: 2019-09-28T00:04:25.041645936Z WARNING:toil.leader:9/w/jobwmLNvl File "get_submission_docker.py", line 15, in
STDERR: 2019-09-28T00:04:25.041764766Z WARNING:toil.leader:9/w/jobwmLNvl raise Exception('Expected DockerRepository type but found '+sub.entity.concreteType)
STDERR: 2019-09-28T00:04:25.041823726Z WARNING:toil.leader:9/w/jobwmLNvl Exception: Expected DockerRepository type but found org.sagebionetworks.repo.model.Project
STDERR: 2019-09-28T00:04:25.041920677Z WARNING:toil.leader:9/w/jobwmLNvl [job get_submission_docker.cwl] Max memory used: 50MiB
STDERR: 2019-09-28T00:04:25.041998527Z WARNING:toil.leader:9/w/jobwmLNvl INFO:cwltool:[job get_submission_docker.cwl] Max memory used: 50MiB
STDERR: 2019-09-28T00:04:25.042106258Z WARNING:toil.leader:9/w/jobwmLNvl [job get_submission_docker.cwl] Job error:
STDERR: 2019-09-28T00:04:25.042172288Z WARNING:toil.leader:9/w/jobwmLNvl Error collecting output for parameter 'docker_repository':
STDERR: 2019-09-28T00:04:25.042280159Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: Expression evaluation error:
STDERR: 2019-09-28T00:04:25.042360949Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: No JSON object could be decoded
STDERR: 2019-09-28T00:04:25.042474540Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: script was:
STDERR: 2019-09-28T00:04:25.042529590Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 01 "use strict";
STDERR: 2019-09-28T00:04:25.042635081Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 02 var inputs = {
STDERR: 2019-09-28T00:04:25.042701120Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 03 "synapse_config": {
STDERR: 2019-09-28T00:04:25.042800922Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 04 "basename": ".synapseConfig",
STDERR: 2019-09-28T00:04:25.042874262Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 05 "nameroot": ".synapseConfig",
STDERR: 2019-09-28T00:04:25.042987142Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 06 "nameext": "",
STDERR: 2019-09-28T00:04:25.043048472Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 07 "location": "toilfs:O/M/tmp3hLSru-x-.synapseConfig",
STDERR: 2019-09-28T00:04:25.043149084Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 08 "path": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8/.synapseConfig",
STDERR: 2019-09-28T00:04:25.043232163Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 09 "dirname": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8",
STDERR: 2019-09-28T00:04:25.043314434Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 10 "class": "File",
STDERR: 2019-09-28T00:04:25.043427614Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 11 "size": 64
STDERR: 2019-09-28T00:04:25.043595616Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 12 },
STDERR: 2019-09-28T00:04:25.043606526Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 13 "submissionid": 9693305
STDERR: 2019-09-28T00:04:25.043708296Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 14 };
STDERR: 2019-09-28T00:04:25.043791447Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 15 var self = [];
STDERR: 2019-09-28T00:04:25.043868417Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 16 var runtime = {
STDERR: 2019-09-28T00:04:25.043956857Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 17 "outdirSize": 1024,
STDERR: 2019-09-28T00:04:25.044029718Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 18 "ram": 100,
STDERR: 2019-09-28T00:04:25.044143588Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 19 "cores": 1,
STDERR: 2019-09-28T00:04:25.044195479Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 20 "tmpdirSize": 1024,
STDERR: 2019-09-28T00:04:25.044327329Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 21 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmp",
STDERR: 2019-09-28T00:04:25.044386399Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 22 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR/8/0/out_tmpdirD1anbF"
STDERR: 2019-09-28T00:04:25.044485401Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 23 };
STDERR: 2019-09-28T00:04:25.044561920Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 24 (function(){return ((JSON.parse(self[0].contents)['docker_repository']));})()
STDERR: 2019-09-28T00:04:25.044655681Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: stdout was: ''
STDERR: 2019-09-28T00:04:25.044727602Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: stderr was: 'evalmachine.:24
STDERR: 2019-09-28T00:04:25.044826412Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: (function(){return ((JSON.parse(self[0].contents)['docker_repository']));})()
STDERR: 2019-09-28T00:04:25.044897572Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: ^
STDERR: 2019-09-28T00:04:25.044989113Z WARNING:toil.leader:9/w/jobwmLNvl :1:1:
STDERR: 2019-09-28T00:04:25.045091793Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: TypeError: Cannot read property 'contents' of undefined
STDERR: 2019-09-28T00:04:25.045161323Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at evalmachine.:24:41
STDERR: 2019-09-28T00:04:25.045243354Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at evalmachine.:24:76
STDERR: 2019-09-28T00:04:25.045327244Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Script.runInContext (vm.js:107:20)
STDERR: 2019-09-28T00:04:25.045410845Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Script.runInNewContext (vm.js:113:17)
STDERR: 2019-09-28T00:04:25.045494926Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Object.runInNewContext (vm.js:296:38)
STDERR: 2019-09-28T00:04:25.045576686Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket. ([eval]:11:57)
STDERR: 2019-09-28T00:04:25.045661546Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket.emit (events.js:189:13)
STDERR: 2019-09-28T00:04:25.045743526Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at addChunk (_stream_readable.js:284:12)
STDERR: 2019-09-28T00:04:25.045826367Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at readableAddChunk (_stream_readable.js:261:13)
STDERR: 2019-09-28T00:04:25.045930008Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket.Readable.push (_stream_readable.js:220:10)'
STDERR: 2019-09-28T00:04:25.045998348Z WARNING:toil.leader:9/w/jobwmLNvl ERROR:cwltool:[job get_submission_docker.cwl] Job error:
STDERR: 2019-09-28T00:04:25.046091358Z WARNING:toil.leader:9/w/jobwmLNvl Error collecting output for parameter 'docker_repository':
STDERR: 2019-09-28T00:04:25.046165909Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: Expression evaluation error:
STDERR: 2019-09-28T00:04:25.046249360Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: No JSON object could be decoded
STDERR: 2019-09-28T00:04:25.046331480Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: script was:
STDERR: 2019-09-28T00:04:25.046423991Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 01 "use strict";
STDERR: 2019-09-28T00:04:25.046497220Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 02 var inputs = {
STDERR: 2019-09-28T00:04:25.046581171Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 03 "synapse_config": {
STDERR: 2019-09-28T00:04:25.046664891Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 04 "basename": ".synapseConfig",
STDERR: 2019-09-28T00:04:25.046746652Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 05 "nameroot": ".synapseConfig",
STDERR: 2019-09-28T00:04:25.046829442Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 06 "nameext": "",
STDERR: 2019-09-28T00:04:25.046921503Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 07 "location": "toilfs:O/M/tmp3hLSru-x-.synapseConfig",
STDERR: 2019-09-28T00:04:25.047005364Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 08 "path": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8/.synapseConfig",
STDERR: 2019-09-28T00:04:25.047082374Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 09 "dirname": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpchDjia/stge96f7cda-24e1-4f11-8f1a-3295994803a8",
STDERR: 2019-09-28T00:04:25.047184724Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 10 "class": "File",
STDERR: 2019-09-28T00:04:25.047258395Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 11 "size": 64
STDERR: 2019-09-28T00:04:25.047351925Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 12 },
STDERR: 2019-09-28T00:04:25.047412706Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 13 "submissionid": 9693305
STDERR: 2019-09-28T00:04:25.047575556Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 14 };
STDERR: 2019-09-28T00:04:25.047614386Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 15 var self = [];
STDERR: 2019-09-28T00:04:25.047728097Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 16 var runtime = {
STDERR: 2019-09-28T00:04:25.047781478Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 17 "outdirSize": 1024,
STDERR: 2019-09-28T00:04:25.047893808Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 18 "ram": 100,
STDERR: 2019-09-28T00:04:25.047944008Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 19 "cores": 1,
STDERR: 2019-09-28T00:04:25.048058618Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 20 "tmpdirSize": 1024,
STDERR: 2019-09-28T00:04:25.048119359Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 21 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmp",
STDERR: 2019-09-28T00:04:25.048224569Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 22 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/502304da-3baa-4fbe-be6d-92ae16bf4096/tmpges6IR/8/0/out_tmpdirD1anbF"
STDERR: 2019-09-28T00:04:25.048300320Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 23 };
STDERR: 2019-09-28T00:04:25.048405770Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: 24 (function(){return ((JSON.parse(self[0].contents)['docker_repository']));})()
STDERR: 2019-09-28T00:04:25.048474681Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: stdout was: ''
STDERR: 2019-09-28T00:04:25.048569911Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: stderr was: 'evalmachine.:24
STDERR: 2019-09-28T00:04:25.048641711Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: (function(){return ((JSON.parse(self[0].contents)['docker_repository']));})()
STDERR: 2019-09-28T00:04:25.048736402Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: ^
STDERR: 2019-09-28T00:04:25.048816672Z WARNING:toil.leader:9/w/jobwmLNvl :1:1:
STDERR: 2019-09-28T00:04:25.048922073Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: TypeError: Cannot read property 'contents' of undefined
STDERR: 2019-09-28T00:04:25.048975684Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at evalmachine.:24:41
STDERR: 2019-09-28T00:04:25.049087784Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at evalmachine.:24:76
STDERR: 2019-09-28T00:04:25.049150024Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Script.runInContext (vm.js:107:20)
STDERR: 2019-09-28T00:04:25.049246685Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Script.runInNewContext (vm.js:113:17)
STDERR: 2019-09-28T00:04:25.049307755Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Object.runInNewContext (vm.js:296:38)
STDERR: 2019-09-28T00:04:25.049421366Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket. ([eval]:11:57)
STDERR: 2019-09-28T00:04:25.049482086Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket.emit (events.js:189:13)
STDERR: 2019-09-28T00:04:25.049577827Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at addChunk (_stream_readable.js:284:12)
STDERR: 2019-09-28T00:04:25.049639427Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at readableAddChunk (_stream_readable.js:261:13)
STDERR: 2019-09-28T00:04:25.049753127Z WARNING:toil.leader:9/w/jobwmLNvl :1:1: at Socket.Readable.push (_stream_readable.js:220:10)'
STDERR: 2019-09-28T00:04:25.049816448Z WARNING:toil.leader:9/w/jobwmLNvl [job get_submission_docker.cwl] completed permanentFail
STDERR: 2019-09-28T00:04:25.049913179Z WARNING:toil.leader:9/w/jobwmLNvl WARNING:cwltool:[job get_submission_docker.cwl] completed permanentFail
STDERR: 2019-09-28T00:04:25.049975579Z WARNING:toil.leader:9/w/jobwmLNvl Traceback (most recent call last):
STDERR: 2019-09-28T00:04:25.050082489Z WARNING:toil.leader:9/w/jobwmLNvl File "/usr/local/lib/python2.7/site-packages/toil/worker.py", line 331, in workerScript
STDERR: 2019-09-28T00:04:25.050143419Z WARNING:toil.leader:9/w/jobwmLNvl job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
STDERR: 2019-09-28T00:04:25.050252800Z WARNING:toil.leader:9/w/jobwmLNvl File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1378, in _runner
STDERR: 2019-09-28T00:04:25.050311711Z WARNING:toil.leader:9/w/jobwmLNvl returnValues = self._run(jobGraph, fileStore)
STDERR: 2019-09-28T00:04:25.050420111Z WARNING:toil.leader:9/w/jobwmLNvl File "/usr/local/lib/python2.7/site-packages/toil/job.py", line 1323, in _run
STDERR: 2019-09-28T00:04:25.050491091Z WARNING:toil.leader:9/w/jobwmLNvl return self.run(fileStore)
STDERR: 2019-09-28T00:04:25.050590402Z WARNING:toil.leader:9/w/jobwmLNvl File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 606, in run
STDERR: 2019-09-28T00:04:25.050651632Z WARNING:toil.leader:9/w/jobwmLNvl raise cwltool.errors.WorkflowException(status)
STDERR: 2019-09-28T00:04:25.050756883Z WARNING:toil.leader:9/w/jobwmLNvl WorkflowException: permanentFail
STDERR: 2019-09-28T00:04:25.050819683Z WARNING:toil.leader:9/w/jobwmLNvl ERROR:toil.worker:Exiting the worker because of a failed job on host 4f92e58f50d9
STDERR: 2019-09-28T00:04:25.050950134Z WARNING:toil.leader:9/w/jobwmLNvl WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl with ID 9/w/jobwmLNvl to 0
STDERR: 2019-09-28T00:04:25.053522187Z WARNING:toil.leader:Job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl with ID 9/w/jobwmLNvl is completely failed
STDERR: 2019-09-28T00:04:25.085580304Z INFO:toil.leader:Job ended successfully: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/notification_email.cwl' python p/G/jobcZamrh
STDERR: 2019-09-28T00:04:30.420822464Z INFO:toil.leader:Finished toil run with 4 failed jobs.
STDERR: 2019-09-28T00:04:30.421146985Z INFO:toil.leader:Failed jobs at end of the run: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/download_from_synapse.cwl' python s/T/job6Vv4HQ 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_docker_config.cwl' python L/l/jobAhrort 'CWLWorkflow' b/6/job8FkZWU 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v1.6/get_submission_docker.cwl' python 9/w/jobwmLNvl
STDERR: 2019-09-28T00:04:30.488893448Z Traceback (most recent call last):
STDERR: 2019-09-28T00:04:30.488920289Z File "/usr/local/bin/toil-cwl-runner", line 10, in
STDERR: 2019-09-28T00:04:30.488925929Z sys.exit(main())
STDERR: 2019-09-28T00:04:30.488930139Z File "/usr/local/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 1276, in main
STDERR: 2019-09-28T00:04:30.489188420Z outobj = toil.start(wf1)
STDERR: 2019-09-28T00:04:30.489218680Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 781, in start
STDERR: 2019-09-28T00:04:30.489387251Z return self._runMainLoop(rootJobGraph)
STDERR: 2019-09-28T00:04:30.489396691Z File "/usr/local/lib/python2.7/site-packages/toil/common.py", line 1054, in _runMainLoop
STDERR: 2019-09-28T00:04:30.489682253Z jobCache=self._jobCache).run()
STDERR: 2019-09-28T00:04:30.489692863Z File "/usr/local/lib/python2.7/site-packages/toil/leader.py", line 246, in run
STDERR: 2019-09-28T00:04:30.489696823Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2019-09-28T00:04:30.489717652Z toil.leader.FailedJobsException
Hi Wendy,
What was the message in the log file? And what log files were created?
Thanks,
Tim
Drop files to upload
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