Job request: 4234

Organisation:: The London School of Hygiene & Tropical Medicine
Workspace:: covid-vaccine-neuro-research
ID:: zcbijnzymesrcyjx

This page shows the technical details of what happened when the authorised researcher John Tazare 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:

SCCS_baseline_tables_AZ

Status:

Status: Failed

Job identifier:

lepyjijm3c74hdx3

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_assumption_checking_AZ

Status:

Status: Failed

Job identifier:

tnvah35fwibyozyz

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_second_dose_AZ

Status:

Status: Failed

Job identifier:

aimowrrhzk77a3mr

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_first_dose_only_primary_MOD

Status:

Status: Failed

Job identifier:

oots2daidn6yicgl

Error:

nonzero_exit: Job exited with an error code
Action:

SCCS_vary_risk_windows_AZ

Status:

Status: Failed

Job identifier:

o7sepshz6zcw22nv

Error:

dependency_failed: Not starting as dependency failed
Action:

apply_exclusion_criteria

Status:

Status: Succeeded

Job identifier:

zjzljmlcalf5wudz
Action:

SCCS_first_dose_only_primary_PF

Status:

Status: Failed

Job identifier:

exmnlawenf3kazbc

Error:

nonzero_exit: Job exited with an error code
Action:

SCCS_stratified_analyses_PF

Status:

Status: Failed

Job identifier:

i3hwidsuass2yj2s

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_vary_risk_windows_PF

Status:

Status: Failed

Job identifier:

j4huibnyijgali6i

Error:

dependency_failed: Not starting as dependency failed
Action:

generate_cohort

Status:

Status: Succeeded

Job identifier:

y6gystyntpnpdj7s
Action:

SCCS_assumption_checking_PF

Status:

Status: Failed

Job identifier:

c7pc6azq47gqgzgp

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_first_dose_only_primary_AZ

Status:

Status: Failed

Job identifier:

mavjgilus2luwsjp

Error:

nonzero_exit: Job exited with an error code
Action:

SCCS_baseline_tables_PF

Status:

Status: Failed

Job identifier:

hsqipqh6juhdto27

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_comparative_AZ_Pfizer

Status:

Status: Failed

Job identifier:

lsymyvvvodbr4n2q

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_second_dose_PF

Status:

Status: Failed

Job identifier:

ct5gdymikddez2hm

Error:

dependency_failed: Not starting as dependency failed
Action:

SCCS_stratified_analyses_AZ

Status:

Status: Failed

Job identifier:

y5qwbv6ekk3aocxb

Error:

dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 5000

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
      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 
        denominators: output/tables/denominators*

  # 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/*

  # 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

Timeline

Created: 3 years, 10 months ago 22 Oct 2021 15:51:37 UTC
Finished: 3 years, 10 months ago 22 Oct 2021 17:40:25 UTC
Runtime:

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: John Tazare
Branch: main
Force run dependencies: Yes
Git commit hash: 3aaefeb
Requested actions: run_all

Code comparison

Compare the code used in this Job Request