Dear Organizer,
What would be the name of the input file containing the combinations to predict for in the /input directory?
Also what would be the file format?
Regards,
Team Resham
Created by Raghvendra Mall raghvendramall @raghvendramall,
Great! If you come across any other issues, please let us know!
Best,
Verena Dear @v.chung,
I managed to fix the issue. Thanks a lot for your prompt response.
Regards,
Raghvendra @raghvendramall,
To best assist, can you let me know of the submission ID(s) that result in the error messages you copied above?
Thank you!
Verena Dear @v.chung ,
While trying to submit a particular model, in my log I see that everything finished correctly but when I check the workflow status in submission dashboard, it shows an error.
What can be a reason for this? I have used the same workflow for submitting other models based on other techniques and they have all been scored.
The log looks like:
STDERR: 2020-02-11T08:10:06.975904909Z 0f75d19695e8 2020-02-11 08:10:06,975 MainThread INFO toil.leader: Failed jobs at end of the run: '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/instancetapmmpyz '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/instance7r75s88y 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/95019517-de7d-4f02-922c-ab44886b67c0/CTD2-BeatAML-Challenge-master/validate_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_95019517-de7d-4f02-922c-ab44886b67c0_CTD2-BeatAML-Challenge-master_validate_email.cwl/instancecff90raj '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/instancezlue9orv 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/95019517-de7d-4f02-922c-ab44886b67c0/CTD2-BeatAML-Challenge-master/validate_sc1.cwl' validate_sc1.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_95019517-de7d-4f02-922c-ab44886b67c0_CTD2-BeatAML-Challenge-master_validate_sc1.cwl/instancer263jnky 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/95019517-de7d-4f02-922c-ab44886b67c0/CTD2-BeatAML-Challenge-master/run_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_95019517-de7d-4f02-922c-ab44886b67c0_CTD2-BeatAML-Challenge-master_run_docker.cwl/instancernb39y98 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/95019517-de7d-4f02-922c-ab44886b67c0/CTD2-BeatAML-Challenge-master/validate_docker.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_95019517-de7d-4f02-922c-ab44886b67c0_CTD2-BeatAML-Challenge-master_validate_docker.cwl/instance1jy31hi3 '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/instance_yzzv_tj 'CWLWorkflow' kind-CWLWorkflow/instancehhye3j0e '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/instanceib4jfo26 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v2.0/upload_to_synapse.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.0_upload_to_synapse.cwl/instancebst9b09c
STDERR: 2020-02-11T08:10:06.989164381Z Traceback (most recent call last):
STDERR: 2020-02-11T08:10:06.989186021Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2020-02-11T08:10:06.989190059Z sys.exit(main())
STDERR: 2020-02-11T08:10:06.989192590Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1357, in main
STDERR: 2020-02-11T08:10:06.989195366Z result = toil.start(wf1)
STDERR: 2020-02-11T08:10:06.989197629Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 800, in start
STDERR: 2020-02-11T08:10:06.989200106Z return self._runMainLoop(rootJobGraph)
STDERR: 2020-02-11T08:10:06.989202259Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1070, in _runMainLoop
STDERR: 2020-02-11T08:10:06.989204647Z jobCache=self._jobCache).run()
STDERR: 2020-02-11T08:10:06.989206716Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 246, in run
STDERR: 2020-02-11T08:10:06.989209104Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2020-02-11T08:10:06.989211386Z toil.leader.FailedJobsException
and is particularly hard to decipher.
Regards,
Raghvendra Dear @raghvendramall,
We are experiencing failed email deliveries to your group, Resham, which most likely is due to the notification settings. To check, please navigate to your team page and click on the three dots, followed by **Edit Team**. In order to receive emails from Synapse, the checkbox (_Any Synapse user can send messages to this team_) must be ticked.
Best,
Verena
Dear Team Resham,
I believe this may have been a [temporary outage](https://www.synapse.org/#!Synapse:syn20940518/discussion/threadId=6710&replyId=21278). Could you try again, and let us know if you have another failure?
Best,
Jacob Dear Moderators,
We are not getting mails for submitted docker images. The submission happens successfully.
Is there an issue ?
Regards,
Team Resham Dear Team Resham,
There is no file explicitly listing the combinations - you should make predictions for *all possible* (lab_id, inhibitor) pairs.
- inhibitors are the same in all datasets - you can get the list of 122 inhibitors from the training set (and store them in your Docker container)
- Specimen lab_ids are available in any of of the input files, eg `/input/clinical_numerical.csv`.
Eg, since there are 80 specimens in the leaderboard dataset, you should have 9760 predictions in your output file.
Best,
Jacob