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Job request: 14872

Organisation:
University of Bristol
Workspace:
post-covid-autoimmune
ID:
ssfhkgd7qvj6ox2e
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Yinghui Wei 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:
    vax_eligibility_inputs
    Status:
    Status: Succeeded
    Job identifier:
    6hxps6wcfwjft23p
  • Action:
    generate_study_population_prelim
    Status:
    Status: Succeeded
    Job identifier:
    o56nufq3kbkmhuf5
  • Action:
    generate_index_dates
    Status:
    Status: Succeeded
    Job identifier:
    wen3xrtco3blipyh
  • Action:
    generate_study_population_vax
    Status:
    Status: Failed
    Job identifier:
    l6xxlygo7pxq2era
    Error:
    nonzero_exit: Job exited with an error: Ran out of memory (limit for this job was 128.00GB)
  • Action:
    generate_study_population_prevax
    Status:
    Status: Failed
    Job identifier:
    md7cmqkfyiwebwqd
    Error:
    nonzero_exit: Job exited with an error: Ran out of memory (limit for this job was 128.00GB)
  • Action:
    generate_study_population_unvax
    Status:
    Status: Failed
    Job identifier:
    ihfwskxw5qqu66oe
    Error:
    nonzero_exit: Job exited with an error: Ran out of memory (limit for this job was 128.00GB)
  • Action:
    preprocess_data_vax
    Status:
    Status: Failed
    Job identifier:
    7ahbjswuto42klf4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    preprocess_data_prevax
    Status:
    Status: Failed
    Job identifier:
    jlxap562ut6awys4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    preprocess_data_unvax
    Status:
    Status: Failed
    Job identifier:
    ze55yfexcisvr5no
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv

  generate_study_population_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax.feather

  generate_study_population_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.feather

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    needs:
    - generate_index_dates
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

  ## Preproces data - prevax 

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_*.txt
        descrive_venn: output/not-for-review/describe_venn_prevax.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  ## Preproces data - vax 

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_*.txt
        descrive_venn: output/not-for-review/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  ## Preproces data - unvax 

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_*.txt
        descrive_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 97:13:18

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

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-autoimmune
Requested by
Yinghui Wei
Branch
main
Force run dependencies
Yes
Git commit hash
1e8602d
Requested actions
  • run_all

Code comparison

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