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Job request: 10371

Organisation:
Bennett Institute
Workspace:
paxlovid_sotrovimab
ID:
xglmbwz5iy6ojuzo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Bang Zheng 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_study_population
    Status:
    Status: Failed
    Job identifier:
    vz5rvpnzp2xu3ogs
    Error:
    nonzero_exit: Job exited with error code 5: Ran out of memory (limit for this job was 128.00GB)
  • Action:
    data_preparation
    Status:
    Status: Failed
    Job identifier:
    6xvzmovv2t6dm6af
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  data_preparation:
    run: stata-mp:latest analysis/data_preparation_and_descriptives.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation.log
      highly_sensitive:
        data: output/main.dta

  cox_regression:
    run: stata-mp:latest analysis/cox.do
    needs: [data_preparation]
    outputs:
      moderately_sensitive:
        log: logs/cox.log
        figure1: output/phtest.svg  
        figure2: output/phtest_psw.svg

  multiple_imputation:
    run: stata-mp:latest analysis/multiple_imputation.do
    needs: [data_preparation]
    outputs:
      moderately_sensitive:
        log: logs/MI.log

  generate_study_population_archive:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_archive
    outputs:
      highly_sensitive:
        cohort: output/archive/input_archive.csv

  data_preparation_archive:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_archive.do
    needs: [generate_study_population_archive]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_archive.log
      highly_sensitive:
        data: output/archive/main_archive.dta

  cox_regression_archive:
    run: stata-mp:latest analysis/cox_archive.do
    needs: [data_preparation_archive]
    outputs:
      moderately_sensitive:
        log: logs/cox_archive.log
        figure1: output/archive/phtest.svg  
        figure2: output/archive/phtest_psw.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 26:19:29

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

Job request

Status
Failed
Backend
TPP
Workspace
paxlovid_sotrovimab
Requested by
Bang Zheng
Branch
main
Force run dependencies
No
Git commit hash
5f33da3
Requested actions
  • generate_study_population
  • data_preparation

Code comparison

Compare the code used in this job request