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Job request: 5064

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vaccine-neuro-research
ID:
bmobomv6mvs5mqsx
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Schultze 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000
  
actions:

  # extract relevant cohorts 
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_sccs_and_historical_cohort.csv

  apply_exclusion_criteria:
    run: stata-mp:latest analysis/apply_exclusion_criteria.do 
    needs: [generate_cohort] 
    outputs:
      moderately_sensitive: 
        log: output/logs/apply_exclusion_criteria.log
        denominators: output/tables/denominators*
      highly_sensitive:
        cohort_controls: output/input_historical_controls.csv
        cohort_az_cases: output/input_AZ_cases.csv
        cohort_pfizer_cases: output/input_PF_cases.csv 
        cohort_moderna_cases: output/input_MOD_cases.csv 

  # main analyses 
  SCCS_first_dose_only_primary_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do AZ
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_AZ.log
        results: output/tables/results_summary_primary_AZ* 
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_AZ*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_AZ*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_AZ*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_AZ*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_AZ*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_AZ*

  SCCS_first_dose_only_primary_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do PF 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_PF.log
        results: output/tables/results_summary_primary_PF*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_PF*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_PF*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_PF*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_PF*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_PF*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_PF*

  SCCS_first_dose_only_primary_MOD:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do MOD 
    needs: [apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_MOD.log
        results: output/tables/results_summary_primary_MOD*
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP_MOD*
        sccs_pop_TM: output/temp_data/sccs_popn_TM_MOD*
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS_MOD*
        sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_MOD*
        sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_MOD*
        sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_MOD*

  # baseline tables (AZ and PF only due to small MOD numbers)
  SCCS_baseline_tables_AZ:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_AZ.log
        tables: output/tables/baseline_AZ/*

  SCCS_baseline_tables_PF:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_PF.log
        tables: output/tables/baseline_PF/*

  SCCS_baseline_tables_MOD:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do MOD
    needs: [SCCS_first_dose_only_primary_MOD] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables_MOD.log
        tables: output/tables/baseline_MOD/*

  # check assumptions 
  SCCS_assumption_checking_AZ:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_AZ.log
        plots_S1: output/plots/S1_exposure_centered_interval_AZ*
        plots_S2: output/plots/S2_censored_futime_AZ*

  SCCS_assumption_checking_PF:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking_PF.log
        plots_S1: output/plots/S1_exposure_centered_interval_PF*
        plots_S2: output/plots/S2_censored_futime_PF*

  # sensitivity analyses 
  ## stratified analyses 
  SCCS_stratified_analyses_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_AZ.log
        results: output/tables/results_summary_stratified_AZ.csv

  SCCS_stratified_analyses_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_PF.log
        results: output/tables/results_summary_stratified_PF.csv

  ## changing risk windows 
  SCCS_vary_risk_windows_AZ:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do AZ
    needs: [SCCS_first_dose_only_primary_AZ] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_AZ.log
        results: output/tables/results_summary_sens_risk_AZ.csv

  SCCS_vary_risk_windows_PF:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do PF
    needs: [SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_PF.log
        results: output/tables/results_summary_sens_risk_PF.csv

  ## second doses 
  SCCS_second_dose_AZ:
    run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_second_dose_analyses_neuro_AZ.log
        results: output/tables/results_summary_second_doses_AZ.csv

  SCCS_second_dose_PF:
    run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_second_dose_analyses_neuro_PF.log
        results: output/tables/results_summary_second_doses_PF*

  ## AZ vs Pfizer 
  SCCS_comparative_AZ_Pfizer:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do 
    needs: [SCCS_first_dose_only_primary_AZ, SCCS_first_dose_only_primary_PF] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.log
        results: output/tables/results_summary_sens_AZ_vs_PF.csv

  ## Check for overlap 
  SCCS_overlap_check_AZ:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do AZ
    needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_AZ.log

  SCCS_overlap_check_PF:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do PF
    needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_PF.log

  SCCS_overlap_check_MOD:
    run: stata-mp:latest analysis/SCCS_check_all_outcome_overlaps_and_distn_source_BP.do MOD
    needs: [SCCS_first_dose_only_primary_MOD, apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_check_all_outcome_overlaps_and_distn_source_BP_MOD.log

  ## Sensitivity - censoring and second dose 
  #   SCCS_censor_2dose_AZ:
  #     run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_censor_at2nd_dose.do AZ
  #     needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
  #     outputs:
  #    moderately_sensitive: 
  #     log: output/logs/SCCS_first_dose_only_sens_censor_at2nd_dose_AZ.log
  #     results: output/tables/results_summary_sens_censor_at2nd_dose_AZ.csv

  # SCCS_censor_2dose_PF:
  # run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_censor_at2nd_dose.do PF
  # needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria] 
  # outputs:
  #   moderately_sensitive: 
  #     log: output/logs/SCCS_first_dose_only_sens_censor_at2nd_dose_PF.log
  #     results: output/tables/results_summary_sens_censor_at2nd_dose_PF.csv

  # SCCS_postvacc2dose_AZ:
  #     run: stata-mp:latest analysis/SCCS_sens_2nd_dose_only_postvaccbase.do AZ
  #     needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria] 
  #     outputs:
  #       moderately_sensitive: 
  #         log: output/logs/SCCS_sens_2nd_dose_only_postvaccbase_AZ.log
  #        results: output/tables/results_summary_sens_2nd_dose_only_postvaccbase_AZ.csv

  #   SCCS_postvacc2dose_PF:
  #     run: stata-mp:latest analysis/SCCS_sens_2nd_dose_only_postvaccbase.do PF
  #     needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria]   
  #     outputs:
  #       moderately_sensitive: 
  #         log: output/logs/SCCS_sens_2nd_dose_only_postvaccbase_PF.log
  #         results: output/tables/results_summary_sens_2nd_dose_only_postvaccbase_PF.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:15:20

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-vaccine-neuro-research
Requested by
Anna Schultze
Branch
main
Force run dependencies
No
Git commit hash
b00eb3f
Requested actions
  • generate_cohort
  • apply_exclusion_criteria
  • SCCS_first_dose_only_primary_AZ
  • SCCS_first_dose_only_primary_PF
  • SCCS_first_dose_only_primary_MOD
  • SCCS_baseline_tables_AZ
  • SCCS_baseline_tables_PF
  • SCCS_baseline_tables_MOD
  • SCCS_second_dose_AZ
  • SCCS_second_dose_PF

Code comparison

Compare the code used in this Job Request