Job request: 10382
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- disect_uk_india_covid
- ID:
- mcnhhgahqkzc5u7s
This page shows the technical details of what happened when the authorised researcher Rohini Mathur 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
-
- Job identifier:
-
5qzis5nq3wanaqbf
-
- Job identifier:
-
nikjhlbrza6ophxp
- Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
qdgnbxkbxmjgd6tj
- Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
brtfxvx4mmkghmmf
- Error:
- nonzero_exit: Job exited with error code 137: Ran out of memory (limit for this job was 128.00GB)
-
- Job identifier:
-
6wb7lyed5naznwg4
- Error:
- nonzero_exit: Job exited with error code 137: Ran out of memory (limit for this job was 128.00GB)
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_w1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_w1
outputs:
highly_sensitive:
cohort: output/input_w1.csv
generate_study_population_w2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_w2
outputs:
highly_sensitive:
cohort: output/input_w2.csv
generate_study_population_w3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_w3
outputs:
highly_sensitive:
cohort: output/input_w3.csv
analyse_w1:
run: r:latest analysis/analysis_wave1_long.R
needs: [generate_study_population_w1]
outputs:
moderately_sensitive:
table1a: output/table1a_w1.csv
table1c: output/table1c_w1.csv
unadjusted_severe: output/unadjusted_severe_w1.csv
unadjusted_long: output/unadjusted_long_w1.csv
# Currently wave 2 is correct so only run W2 scripts in jobs runner
analyse_w2_long:
run: r:latest analysis/analysis_wave2_long.R
needs: [generate_study_population_w2]
outputs:
moderately_sensitive:
table1a_long: output/table1a_w2_long.csv
table1b_long: output/table1b_w2_long.csv
long_incidence: output/long_incidence_w2.csv
long_incidence_strata: output/long_incidence_strata_w2.csv
unadjusted_long: output/unadjusted_long_w2.csv
analyse_w2_severe:
run: r:latest analysis/analysis_wave2_severe.R
needs: [generate_study_population_w2]
outputs:
moderately_sensitive:
table1a: output/table1a_w2.csv
table1b: output/table1b_w2.csv
severe_incidence: output/severe_incidence_w2.csv
severe_incidence_strata: output/severe_incidence_strata_w2.csv
unadjusted_long: output/unadjusted_severe_w2.csv
data_check_w2:
run: r:latest analysis/analysis_wave2_checks.R
needs: [generate_study_population_w2]
outputs:
moderately_sensitive:
sample_size_table: output/sample_size_table_w2.csv
missing_nums: output/missing_nums_w2.csv
continuous_checks: output/continuous_checks_w2.csv
dates_dmy: output/dates_dmy_w2.csv
dates_my: output/dates_my_w2.csv
binary_checks: output/binary_checks_w2.csv
eth_tab: output/ethnicity5_w2.csv
eth16_tab: output/ethnicity16_w2.csv
sex_tab: output/sex_w2.csv
smoke_tab: output/smoke_w2.csv
imd_tab: output/imd_w2.csv
stp_tab: output/stp_w2.csv
region_tab: output/region_w2.csv
diabetes_tab: output/diabetes_w2.csv
carehome_tab: output/carehome_w2.csv
covid_diagnosis_tab: output/covid_diagnosis_w2.csv
analyse_w3:
run: r:latest analysis/analysis_wave3_long.R
needs: [generate_study_population_w3]
outputs:
moderately_sensitive:
table1a: output/table1a_w3.csv
table1c: output/table1c_w3.csv
unadjusted_severe: output/unadjusted_severe_w3.csv
unadjusted_long: output/unadjusted_long_w3.csv
Timeline
-
Created:
-
Started:
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Finished:
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Runtime: 07:19:40
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
- Backend
- TPP
- Workspace
- disect_uk_india_covid
- Requested by
- Rohini Mathur
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- d3d8083
- Requested actions
-
-
generate_study_population_w1
-
generate_study_population_w2
-
generate_study_population_w3
-
analyse_w2_long
-
analyse_w2_severe
-
Code comparison
Compare the code used in this job request