Extract Cohort optimizations [VS-493] [VS-1516] #4942
Triggered via pull request
December 4, 2024 21:18
mcovarr
Status
Failure
Total duration
3h 16m 35s
Artifacts
3
gatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
8m 31s
Validate script WDLs using womtools
50s
Validate generated WDLs using womtools
13m 11s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
8 errors and 14 warnings
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build and push gatk docker to artifacts
buildx failed with: ERROR: failed to solve: process "/bin/sh -c add-apt-repository -y ppa:ubuntu-toolchain-r/test && apt-get update && apt-get -y upgrade libstdc++6 && apt-get -y dist-upgrade" did not complete successfully: exit code: 1
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Java 17.0.6+10 build and test cloud
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
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Java 17.0.6+10 build and test cloud
The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/setup-gcloud
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Java 17.0.6+10 build and test unit
The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/setup-gcloud
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Java 17.0.6+10 build and test unit
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
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Java 17.0.6+10 build and test integration
The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/auth
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Java 17.0.6+10 build and test integration
The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions:
https://github.com/google-github-actions/setup-gcloud
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WDL test RUN_CNN_WDL on cromwell
Process completed with exit code 1.
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check if the environment has privileges
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Validate script WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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build and push gatk docker to artifacts
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Validate generated WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 build and test cloud
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 build and test unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 build and test integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_M2_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNN_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Deprecation notice: v1, v2, and v3 of the artifact actions
The following artifacts were uploaded using a version of actions/upload-artifact that is scheduled for deprecation: "test-results-17.0.6+10-cloud", "test-results-17.0.6+10-integration", "test-results-17.0.6+10-unit".
Please update your workflow to use v4 of the artifact actions.
Learn more: https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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test-results-17.0.6+10-cloud
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333 KB |
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test-results-17.0.6+10-integration
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3.46 MB |
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test-results-17.0.6+10-unit
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157 MB |
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