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Job request: 19394

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
safety-sotrovimab-paxlovid-molnupiravir
ID:
2jmindrar4nikie4
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Katie Bechman 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:
    cox_model
    Status:
    Status: Failed
    Job identifier:
    n7litcvkr2in2sno

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:

  generate_study_population_control:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control
    outputs:
      highly_sensitive:
        cohort: output/input_control.csv
        
  generate_study_population_treatment:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treatment
    outputs:
      highly_sensitive:
        cohort: output/input_treatment.csv

  data_properties:
    run: r:latest analysis/data_properties.R output/input_control.csv output/input_treatment.csv output/data_properties
    needs: [generate_study_population_control, generate_study_population_treatment]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/input*.txt

  define_covariates_combine:
    run: stata-mp:latest analysis/002_define_covariates_combine.do
    needs: [generate_study_population_control, generate_study_population_treatment]
    outputs:
      moderately_sensitive:
        log: logs/cleaning_dataset_combine_2.log 
      highly_sensitive:
        data: output/data/main.dta

  baseline_characteristic:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/baseline_characterisitcs.log 
        data: output/tables/baseline_allpts.csv      

  cox_model:
    run: stata-mp:latest analysis/200_cox_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/cox_model.log 
        data: output/tables/cox_model_summary_csv.csv 
        survrisk_ae_all: output/figures/survrisk_ae_all.svg
        survrisk_allcause_emerg_aande: output/figures/survrisk_allcause_emerg_aande.svg
        survrisk_covid_hosp_date: output/figures/survrisk_covid_hosp_date.svg
        survrisk_all_hosp_date: output/figures/survrisk_all_hosp_date.svg
        survrisk_died_date_ons: output/figures/survrisk_died_date_ons.svg
        survcur_ae_all: output/figures/survcur_ae_all.svg
        survcur_allcause_emerg_aande: output/figures/survcur_allcause_emerg_aande.svg
        survcur_covid_hosp_date: output/figures/survcur_covid_hosp_date.svg
        survcur_all_hosp_date: output/figures/survcur_all_hosp_date.svg
        survcur_died_date_ons: output/figures/survcur_died_date_ons.svg
        

  PS_model:
    run: stata-mp:latest analysis/300_ps_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/ps_model.log
        data: output/tables/cox_model_propensity_csv.csv 
        histogram_agesex: output/figures/histogram_agesex.svg
        histogram_adj: output/figures/histogram_adj.svg
        histogram_fuladj1: output/figures/histogram_fulladj1.svg
        histogram_fulladj2: output/figures/histogram_fulladj2.svg
        match_agesex: output/figures/match_agesex.svg
        match_adj: output/figures/match_adj.svg
  
  preceed_rate:
    run: stata-mp:latest analysis/400_preceeding_rate.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/preceed_rate.log 
        data: output/tables/comparator_rate_summary_csv.csv 
  
  redacted_table:
    run: stata-mp:latest analysis/500_redacted_table.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log1: logs/redacted_table.log   
        doc1: output/tables/baseline_table_redact_bydrug.csv   
        doc2: output/tables/baseline_table_redact_mean.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:39:21

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

Job information

Status
Failed
Backend
TPP
Workspace
safety-sotrovimab-paxlovid-molnupiravir
Requested by
Katie Bechman
Branch
main
Force run dependencies
No
Git commit hash
4ac6e5d
Requested actions
  • cox_model

Code comparison

Compare the code used in this Job Request