Job request: 18980
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- safety-sotrovimab-paxlovid-molnupiravir
- ID:
- nldsyapahdlbax5s
This page shows the technical details of what happened when the authorised researcher Millie Green 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
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- Job identifier:
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4vbxtwbf7geulwjk
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- Job identifier:
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3m3gsbplnw5lofm3 - Error:
- nonzero_exit: Job exited with an error: Something went wrong with the database, please contact tech support
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- Job identifier:
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lu66ywcrzvix5nel - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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rbsawcvcz4ywwy2a - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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c4pnh4ji3hrs64wf - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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k7fxg45r32pmwnks - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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d4ppzga337msnyku - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
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hnvltiox4mew66ya - Error:
- dependency_failed: Not starting as dependency failed
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/001_define_covariates_combine.do
needs: [generate_study_population_control, generate_study_population_treatment]
outputs:
moderately_sensitive:
log: logs/cleaning_dataset_combine.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
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.dta
survrisk_ae_all: output/figures/survrisk_ae_all.svg
survrisk_ae_spc_all: output/figures/survrisk_ae_spc_all.svg
survrisk_ae_drug_all: output/figures/survrisk_ae_drug_all.svg
survrisk_ae_imae_all: output/figures/survrisk_ae_imae_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
survhaz_ae_all: output/figures/survhaz_ae_all.svg
survhaz_ae_spc_all: output/figures/survhaz_ae_spc_all.svg
survhaz_ae_drug_all: output/figures/survhaz_ae_drug_all.svg
survhaz_ae_imae_all: output/figures/survhaz_ae_imae_all.svg
survhaz_allcause_emerg_aande: output/figures/survhaz_allcause_emerg_aande.svg
survhaz_covid_hosp_date: output/figures/survhaz_covid_hosp_date.svg
survhaz_all_hosp_date: output/figures/survhaz_all_hosp_date.svg
survhaz_died_date_ons: output/figures/survhaz_died_date_ons.svg
survcur_ae_all: output/figures/survcur_ae_all.svg
survcur_ae_spc_all: output/figures/survcur_ae_spc_all.svg
survcur_ae_drug_all: output/figures/survcur_ae_drug_all.svg
survcur_ae_imae_all: output/figures/survcur_ae_imae_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.dta
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
match_fulladj1: output/figures/match_fulladj1.svg
match_fulladj2: output/figures/match_fulladj2.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.dta
Timeline
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Created:
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Started:
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Finished:
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Runtime: 205:17:54
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
- Backend
- TPP
- Workspace
- safety-sotrovimab-paxlovid-molnupiravir
- Requested by
- Millie Green
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 094b443
- Requested actions
-
-
generate_study_population_control -
generate_study_population_treatment -
data_properties -
define_covariates_combine -
baseline_characteristic -
cox_model -
PS_model -
preceed_rate
-
Code comparison
Compare the code used in this job request