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Job request: 1095

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_doses
ID:
2sls74nsmmcinvy7
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    data_properties_over80s
    Status:
    Status: Failed
    Job identifier:
    ekxhncqlgz24s5pu
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_eventsperday_over80s
    Status:
    Status: Failed
    Job identifier:
    v5hjuwb66owfngrs
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    descr_table1_over80s
    Status:
    Status: Failed
    Job identifier:
    onm7gi6bi3kkau37
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    models_msm_over80s
    Status:
    Status: Failed
    Job identifier:
    cmzis2hfn6ntxpak
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    reportmodels_msm_over80s
    Status:
    Status: Failed
    Job identifier:
    jl5jght3kxltqpfe
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  extract_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all
    outputs:
      highly_sensitive:
        cohort: output/input_all.csv

  data_process_all:
    run: r:latest analysis/R/data_process_all.R
    needs: [extract_all]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_long_vax_dates.rds
        data3: output/data/data_long_admission_dates.rds

  data_properties_all:
    run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process_all]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt

  data_define_cohorts:
    run: r:latest analysis/R/data_define_cohorts.R
    needs: [data_process_all]
    outputs:
      highly_sensitive:
        data: output/data/data_cohorts.rds
      moderately_sensitive:
        metadata: output/data/metadata_cohorts.rds

  ## VE models in over 80s

  data_stset_over80s:
    run: r:latest analysis/R/data_stset.R over80s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      highly_sensitive:
        data: output/over80s/data/data_*.rds

  data_properties_over80s:
    run: r:latest analysis/R/data_properties.R output/over80s/postest/data/data_wide.rds output/over80s/postest/data_properties
    needs: [data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/cohort/outcome/data_properties/data_wide*.txt

  descr_eventsperday_over80s:
    run: r:latest analysis/R/plot_outcomes_per_day.R over80s postest
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/over80s/postest/descr/events*.svg


  descr_table1_over80s:
    run: r:latest analysis/R/table1.R over80s
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      moderately_sensitive:
        table1: output/over80s/descr/table*

  models_msm_over80s:
    run: r:latest analysis/R/models_msms.R over80s postest
    needs: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/modes/model*.rds
        data: output/over80s/postest/models/data_weights.rds
      moderately_sensitive:
        weights: output/over80s/postest/weights.txt
        weightsplot: output/over80s/postest/histogram_weights.svg

  reportmodels_msm_over80s:
    run: r:latest analysis/R/reportmodels_msms.R over80s postest
    needs: [data_define_cohorts, models_msm_over80s]
    outputs:
      moderately_sensitive:
        forest: output/over80s/postest/models/forest*.svg
        trend: output/over80s/postest/models/secular_trends*.svg
        eventrate: output/over80s/postest/models/event_rate.svg
        cmleffect: output/over80s/postest/models/cml_effectiveness.svg
        tables: output/over80s/postest/models/*.csv


  # data_stset_under65s:
  #   run: r:latest analysis/R/data_stset.R under65s
  #   needs: [data_cohorts, data_process_all]
  #   outputs:
  #     highly_sensitive:
  #       data: output/modeldata/data_*under65s.rds
  #
  # data_properties_under65s:
  #   run: r:latest analysis/R/data_properties.R output/modeldata/data_wide_under65s.rds output/data_properties
  #   needs: [data_stset_under65s]
  #   outputs:
  #     moderately_sensitive:
  #       datasummary: output/data_properties/data_wide_under65s*.txt
  #
  # models_msm_under65s:
  #   run: r:latest analysis/R/models_msms.R under65s
  #   needs: [data_cohorts, data_stset_under65s]
  #   outputs:
  #     moderately_sensitive:
  #       weights: output/models/msm/under65s/weights.txt
  #       forest: output/models/msm/under65s/forest*.svg
  #       trend: output/models/msm/under65s/secular_trends*.svg
  #       tables: output/models/msm/under65s/*.csv


  # models_cox_over80s:
  #   run: r:latest analysis/R/models_cox_over80s.R
  #   needs: [data_stset_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       zph: output/models/cox/over80s/zph*.png
  #       forest: output/models/cox/over80s/forest*.svg
  #       tables: output/models/cox/over80s/*.csv


  # run_ve:
  #   run: cohortextractor:latest --version
  #   needs: [extract_all, data_process_all, data_properties_all, data_tte_over80s, models_cox_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       whatever: output/.gitignore

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:03:25

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_doses
Requested by
Will Hulme
Branch
doses
Force run dependencies
No
Git commit hash
16fdaa9
Requested actions
  • data_properties_over80s
  • descr_eventsperday_over80s
  • descr_table1_over80s
  • models_msm_over80s
  • reportmodels_msm_over80s

Code comparison

Compare the code used in this job request