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 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:

extract

Status:

Succeeded

Job identifier:

p345xcxeli5cb5qf
Action:

data_process

Status:

Succeeded

Job identifier:

xqcyxuexnzngokmo
Action:

data_process_long

Status:

Succeeded

Job identifier:

dfbrdrdfms42x5lc
Action:

data_selection

Status:

Succeeded

Job identifier:

glpiqdhw2pjavter
Action:

model_seqtrialcox_pfizer_postest

Status:

Succeeded

Job identifier:

5borrpqtmliqhdlm
Action:

model_seqtrialcox_moderna_postest

Status:

Failed

Job identifier:

qagmy3zwhz4psjzi

Error:

nonzero_exit: Job exited with an error code
Action:

model_seqtrialcox_az_covidadmitted

Status:

Succeeded

Job identifier:

llshmfzleeyc6rd4
Action:

model_seqtrialcox_az_postest

Status:

Succeeded

Job identifier:

lhp4lclnxw7oz4gy
Action:

model_seqtrialcox_az_coviddeath

Status:

Failed

Job identifier:

6r5gaccml7oo42ut

Error:

nonzero_exit: Job exited with an error code
Action:

model_seqtrialcox_moderna_covidadmitted

Status:

Failed

Job identifier:

c4fzvwxnui5y4567

Error:

nonzero_exit: Job exited with an error code
Action:

model_seqtrialcox_moderna_coviddeath

Status:

Failed

Job identifier:

ymr6qo2go5uw3ty4

Error:

nonzero_exit: Job exited with an error code
Action:

model_seqtrialcox_pfizer_coviddeath

Status:

Failed

Job identifier:

5bgngj376w44byyo

Error:

nonzero_exit: Job exited with an error code
Action:

model_seqtrialcox_pfizer_covidadmitted

Status:

Failed

Job identifier:

ompahqwggi5cmmiw

Error:

nonzero_exit: Job exited with an error code
Action:

report_seqtrialcox_az_covidadmitted

Status:

Succeeded

Job identifier:

n5gftfksvp4upenw
Action:

report_seqtrialcox_az_postest

Status:

Succeeded

Job identifier:

oe62rvf74wrdbzkb
Action:

report_seqtrialcox_pfizer_postest

Status:

Succeeded

Job identifier:

xhwj4p3gz476gzwp
Action:

report_seqtrialcox_moderna_coviddeath

Status:

Failed

Job identifier:

cm5nm6is424ksc3n

Error:

dependency_failed: Not starting as dependency failed
Action:

report_seqtrialcox_pfizer_covidadmitted

Status:

Failed

Job identifier:

4ehpzs444quxusqm

Error:

dependency_failed: Not starting as dependency failed
Action:

report_seqtrialcox_pfizer_coviddeath

Status:

Failed

Job identifier:

5fjojefepxa3jd4p

Error:

dependency_failed: Not starting as dependency failed
Action:

report_seqtrialcox_moderna_covidadmitted

Status:

Failed

Job identifier:

56gcut3gcm5t6cpy

Error:

dependency_failed: Not starting as dependency failed
Action:

report_seqtrialcox_az_coviddeath

Status:

Failed

Job identifier:

52ngl5wz4s2hugyi

Error:

dependency_failed: Not starting as dependency failed
Action:

report_seqtrialcox_moderna_postest

Status:

Failed

Job identifier:

mfmaymbhqotw6zjy

Error:

dependency_failed: Not starting as dependency failed

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: 4 years, 3 months ago 15 Jan 2022 20:58:06 UTC
Started: 4 years, 3 months ago 15 Jan 2022 20:58:15 UTC
Finished: 4 years, 3 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 request

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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