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Job request: 16584

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt_longcovid_vaccines
ID:
iugmjt46jfm4rl5h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson 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:
    generate_dataset_controls
    Status:
    Status: Succeeded
    Job identifier:
    o7qur5glyzedc272
  • Action:
    generate_dataset_cases
    Status:
    Status: Succeeded
    Job identifier:
    ishqgrpk4cjr6scu
  • Action:
    basic_analysis
    Status:
    Status: Failed
    Job identifier:
    ackjba4ovkeakvti
    Error:
    nonzero_exit: Job exited with an error: Ran out of memory (limit for this job was 128.00GB)

Pipeline

Show project.yaml 
version: '3.0'

expectations:
 population_size: 1000

actions:

  generate_dataset_cases:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_cases.py --output output/dataset_cases.csv.gz
    outputs:
      highly_sensitive:
        dataset_cases: output/dataset_cases.csv.gz
  
  generate_dataset_controls:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_controls.py --output output/dataset_controls.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_controls.csv.gz
  
  generate_dataset_lc_pre_vacc:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_longcovid_prevaccine.py --output output/dataset_lc_pre_vacc.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_lc_pre_vacc.csv.gz
  
  # quick_checks: 
  #   run: >
  #     r:latest
  #       analysis/010_quick_checks.R
  #   needs: [generate_dataset_cases, generate_dataset_controls, generate_dataset_lc_pre_vacc]
  #   outputs:
  #      moderately_sensitive:
  #        checks: output/010_quick_checks.html
  
  basic_analysis: 
    run: > 
      r:latest
        analysis/001_targets_style_master.R
    needs: [generate_dataset_cases, generate_dataset_controls]
    outputs:
       moderately_sensitive:
         cruderates: output/tab021_crude_lc_rates.csv
         tuvrates:  output/tab022_tuv_lc_rates.csv
         poissonrates: output/tab023_poissonrates.csv
         cuminc: output/fig1_cumulative_incidence.pdf
         rawcountsplot: output/fig2_raw_counts_bysex.pdf
         irrplot: output/fig3_rate_ratios.pdf
         # timeplot:

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:31:34

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

Job request

Status
Failed
Backend
TPP
Workspace
openprompt_longcovid_vaccines
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
Yes
Git commit hash
3ea9cbd
Requested actions
  • generate_dataset_cases
  • generate_dataset_controls
  • basic_analysis

Code comparison

Compare the code used in this job request