Job request: 4941

Organisation:: Bennett Institute
Workspace:: booster-effectiveness_main
ID:: diffcolryodgvea4

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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Action:

extract

Status:

Status: Succeeded

Job identifier:

p345xcxeli5cb5qf
Action:

data_process

Status:

Status: Succeeded

Job identifier:

xqcyxuexnzngokmo
Action:

data_process_long

Status:

Status: Succeeded

Job identifier:

dfbrdrdfms42x5lc
Action:

data_selection

Status:

Status: Succeeded

Job identifier:

glpiqdhw2pjavter
Action:

model_seqtrialcox_pfizer_postest

Status:

Status: Succeeded

Job identifier:

5borrpqtmliqhdlm
Action:

model_seqtrialcox_moderna_postest

Status:

Status: Failed

Job identifier:

qagmy3zwhz4psjzi
Action:

model_seqtrialcox_az_covidadmitted

Status:

Status: Succeeded

Job identifier:

llshmfzleeyc6rd4
Action:

model_seqtrialcox_az_postest

Status:

Status: Succeeded

Job identifier:

lhp4lclnxw7oz4gy
Action:

model_seqtrialcox_az_coviddeath

Status:

Status: Failed

Job identifier:

6r5gaccml7oo42ut
Action:

model_seqtrialcox_moderna_covidadmitted

Status:

Status: Failed

Job identifier:

c4fzvwxnui5y4567
Action:

model_seqtrialcox_moderna_coviddeath

Status:

Status: Failed

Job identifier:

ymr6qo2go5uw3ty4
Action:

model_seqtrialcox_pfizer_coviddeath

Status:

Status: Failed

Job identifier:

5bgngj376w44byyo
Action:

model_seqtrialcox_pfizer_covidadmitted

Status:

Status: Failed

Job identifier:

ompahqwggi5cmmiw
Action:

report_seqtrialcox_az_covidadmitted

Status:

Status: Succeeded

Job identifier:

n5gftfksvp4upenw
Action:

report_seqtrialcox_az_postest

Status:

Status: Succeeded

Job identifier:

oe62rvf74wrdbzkb
Action:

report_seqtrialcox_pfizer_postest

Status:

Status: Succeeded

Job identifier:

xhwj4p3gz476gzwp
Action:

report_seqtrialcox_moderna_coviddeath

Status:

Status: Failed

Job identifier:

cm5nm6is424ksc3n
Action:

report_seqtrialcox_pfizer_covidadmitted

Status:

Status: Failed

Job identifier:

4ehpzs444quxusqm
Action:

report_seqtrialcox_pfizer_coviddeath

Status:

Status: Failed

Job identifier:

5fjojefepxa3jd4p
Action:

report_seqtrialcox_moderna_covidadmitted

Status:

Status: Failed

Job identifier:

56gcut3gcm5t6cpy
Action:

report_seqtrialcox_az_coviddeath

Status:

Status: Failed

Job identifier:

52ngl5wz4s2hugyi
Action:

report_seqtrialcox_moderna_postest

Status:

Status: Failed

Job identifier:

mfmaymbhqotw6zjy

Pipeline

Show project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Pre-server scripts 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Extract and tidy 
  ## # # # # # # # # # # # # # # # # # # # 

  extract:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs: []
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  data_process:
    run: r:latest analysis/data_process.R
    needs:
    - extract
    outputs:
      highly_sensitive:
        processed: output/data/data_processed.rds
        vaxlong: output/data/data_vaxlong.rds

  data_process_long:
    run: r:latest analysis/data_process_long.R
    needs:
    - data_process
    outputs:
      highly_sensitive:
        processed: output/data/data_long*.rds

  data_selection:
    run: r:latest analysis/data_selection.R
    needs:
    - data_process
    outputs:
      highly_sensitive:
        data: output/data/data_cohort.rds
      moderately_sensitive:
        flow: output/data/flowchart.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## Descriptive stats 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Models 
  ## # # # # # # # # # # # # # # # # # # # 
  ## ###  Positive SARS-CoV-2 Test 

  model_seqtrialcox_pfizer_postest:
    run: r:latest analysis/model_seqtrialcox.R pfizer postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/postest/model_*.txt
        csv: output/models/seqtrialcox/pfizer/postest/model_*.csv

  report_seqtrialcox_pfizer_postest:
    run: r:latest analysis/report_seqtrialcox.R pfizer postest
    needs:
    - model_seqtrialcox_pfizer_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/postest/report_*.csv
        svg: output/models/seqtrialcox/pfizer/postest/report_*.svg
        png: output/models/seqtrialcox/pfizer/postest/report_*.png

  model_seqtrialcox_az_postest:
    run: r:latest analysis/model_seqtrialcox.R az postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/postest/model_*.txt
        csv: output/models/seqtrialcox/az/postest/model_*.csv

  report_seqtrialcox_az_postest:
    run: r:latest analysis/report_seqtrialcox.R az postest
    needs:
    - model_seqtrialcox_az_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/postest/report_*.csv
        svg: output/models/seqtrialcox/az/postest/report_*.svg
        png: output/models/seqtrialcox/az/postest/report_*.png

  model_seqtrialcox_moderna_postest:
    run: r:latest analysis/model_seqtrialcox.R moderna postest
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/postest/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/postest/model_*.txt
        csv: output/models/seqtrialcox/moderna/postest/model_*.csv

  report_seqtrialcox_moderna_postest:
    run: r:latest analysis/report_seqtrialcox.R moderna postest
    needs:
    - model_seqtrialcox_moderna_postest
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/postest/report_*.csv
        svg: output/models/seqtrialcox/moderna/postest/report_*.svg
        png: output/models/seqtrialcox/moderna/postest/report_*.png

  ## ###  COVID-19 unplanned admission 

  model_seqtrialcox_pfizer_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R pfizer covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/pfizer/covidadmitted/model_*.csv

  report_seqtrialcox_pfizer_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R pfizer covidadmitted
    needs:
    - model_seqtrialcox_pfizer_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/pfizer/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/pfizer/covidadmitted/report_*.png

  model_seqtrialcox_az_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R az covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/az/covidadmitted/model_*.csv

  report_seqtrialcox_az_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R az covidadmitted
    needs:
    - model_seqtrialcox_az_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/az/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/az/covidadmitted/report_*.png

  model_seqtrialcox_moderna_covidadmitted:
    run: r:latest analysis/model_seqtrialcox.R moderna covidadmitted
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/covidadmitted/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/covidadmitted/model_*.txt
        csv: output/models/seqtrialcox/moderna/covidadmitted/model_*.csv

  report_seqtrialcox_moderna_covidadmitted:
    run: r:latest analysis/report_seqtrialcox.R moderna covidadmitted
    needs:
    - model_seqtrialcox_moderna_covidadmitted
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/covidadmitted/report_*.csv
        svg: output/models/seqtrialcox/moderna/covidadmitted/report_*.svg
        png: output/models/seqtrialcox/moderna/covidadmitted/report_*.png

  ## ###  COVID-19 death 

  model_seqtrialcox_pfizer_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R pfizer coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/pfizer/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/pfizer/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/pfizer/coviddeath/model_*.csv

  report_seqtrialcox_pfizer_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R pfizer coviddeath
    needs:
    - model_seqtrialcox_pfizer_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/pfizer/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/pfizer/coviddeath/report_*.svg
        png: output/models/seqtrialcox/pfizer/coviddeath/report_*.png

  model_seqtrialcox_az_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R az coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/az/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/az/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/az/coviddeath/model_*.csv

  report_seqtrialcox_az_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R az coviddeath
    needs:
    - model_seqtrialcox_az_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/az/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/az/coviddeath/report_*.svg
        png: output/models/seqtrialcox/az/coviddeath/report_*.png

  model_seqtrialcox_moderna_coviddeath:
    run: r:latest analysis/model_seqtrialcox.R moderna coviddeath
    needs:
    - data_selection
    - data_process_long
    outputs:
      highly_sensitive:
        rds: output/models/seqtrialcox/moderna/coviddeath/model_*.rds
      moderately_sensitive:
        txt: output/models/seqtrialcox/moderna/coviddeath/model_*.txt
        csv: output/models/seqtrialcox/moderna/coviddeath/model_*.csv

  report_seqtrialcox_moderna_coviddeath:
    run: r:latest analysis/report_seqtrialcox.R moderna coviddeath
    needs:
    - model_seqtrialcox_moderna_coviddeath
    outputs:
      moderately_sensitive:
        csv: output/models/seqtrialcox/moderna/coviddeath/report_*.csv
        svg: output/models/seqtrialcox/moderna/coviddeath/report_*.svg
        png: output/models/seqtrialcox/moderna/coviddeath/report_*.png

  ## # # # # # # # # # # # # # # # # # # # 
  ## Reports 
  ## # # # # # # # # # # # # # # # # # # #

Timeline

Created: 2 years, 10 months ago 15 Jan 2022 20:58:06 UTC
Started: 2 years, 10 months ago 15 Jan 2022 20:58:15 UTC
Finished: 2 years, 10 months ago 16 Jan 2022 07:09:38 UTC
Runtime: 18:30:59

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

Job information

Status: Failed
Backend: TPP
Workspace: booster-effectiveness_main
Requested by: Will Hulme
Branch: main
Force run dependencies: Yes
Git commit hash: fc5a48c
Requested actions: run_all

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