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 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:

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: 4 years ago 22 Oct 2021 15:51:37 UTC
Finished: 4 years ago 22 Oct 2021 17:40:25 UTC
Runtime:

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

Job request

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