Job request: 4937

Organisation:: Bennett Institute
Workspace:: booster-effectiveness_main
ID:: 7loxfch7gf6oh4iq

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: Failed

Job identifier:

6w6zhrcmzhciyb2k
Action:

model_seqtrialcox_az_postest

Status:

Status: Failed

Job identifier:

7tw6uac2yjn2x2es
Action:

report_seqtrialcox_az_postest

Status:

Status: Failed

Job identifier:

mfuejkoi3gl4vgpp
Action:

model_seqtrialcox_moderna_postest

Status:

Status: Failed

Job identifier:

nyk34mxcpshmfdf3
Action:

model_seqtrialcox_pfizer_covidadmitted

Status:

Status: Failed

Job identifier:

wsrzgq2bag7nemh7
Action:

data_process

Status:

Status: Failed

Job identifier:

kptu5wgk3i4nbgru
Action:

data_process_long

Status:

Status: Failed

Job identifier:

ttarvpwstsrqnn6b
Action:

data_selection

Status:

Status: Failed

Job identifier:

qvmv3ef6juibrml4
Action:

report_seqtrialcox_pfizer_covidadmitted

Status:

Status: Failed

Job identifier:

zspkpwdwro6qlaxp
Action:

model_seqtrialcox_az_covidadmitted

Status:

Status: Failed

Job identifier:

yyapxaxly2csvysd
Action:

model_seqtrialcox_moderna_covidadmitted

Status:

Status: Failed

Job identifier:

cznui6773bysnkod
Action:

report_seqtrialcox_moderna_covidadmitted

Status:

Status: Failed

Job identifier:

rxl4le6kldcqylj3
Action:

model_seqtrialcox_pfizer_coviddeath

Status:

Status: Failed

Job identifier:

f752py2pcvu2f2c2
Action:

report_seqtrialcox_pfizer_coviddeath

Status:

Status: Failed

Job identifier:

ltxvk5snqncujfzq
Action:

report_seqtrialcox_az_coviddeath

Status:

Status: Failed

Job identifier:

zfsbzqqeknvc57g3
Action:

model_seqtrialcox_moderna_coviddeath

Status:

Status: Failed

Job identifier:

v72xbzmfvftcs2fb
Action:

report_seqtrialcox_moderna_coviddeath

Status:

Status: Failed

Job identifier:

tlfspbsgnxarpdxy
Action:

model_seqtrialcox_pfizer_postest

Status:

Status: Failed

Job identifier:

pfwxmcnufquinabo
Action:

report_seqtrialcox_moderna_postest

Status:

Status: Failed

Job identifier:

zg6mogzlick7jqt2
Action:

report_seqtrialcox_az_covidadmitted

Status:

Status: Failed

Job identifier:

ctbmmgvugxngutls
Action:

report_seqtrialcox_pfizer_postest

Status:

Status: Failed

Job identifier:

fy4yr3f5kike5hth
Action:

model_seqtrialcox_az_coviddeath

Status:

Status: Failed

Job identifier:

otu64bm5bny3itew

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 14 Jan 2022 20:41:02 UTC
Started: 2 years, 10 months ago 15 Jan 2022 05:23:46 UTC
Finished: 2 years, 10 months ago 15 Jan 2022 05:27:00 UTC
Runtime: 00:02:36

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: No
Git commit hash: b544bcd
Requested actions: run_all

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