Build and Test GATK 4

GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #3982

Sign in to view logs

Triggered via pull request April 2, 2024 14:06

ldgauthier

synchronize #8741

ldg_fix_all_sites_no_calls

Status Failure

Total duration 2h 52m 28s

Artifacts 8

gatk-tests.yml

on: pull_request

check if the environment has privileges

build and push gatk docker to artifacts

Validate script WDLs using womtools

Validate generated WDLs using womtools

Matrix: wdlTests

Matrix: test

Matrix: testOnDocker

Annotations

12 errors and 16 warnings

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The v0 series of google-github-actions/auth is no longer maintained.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

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The v0 series of google-github-actions/auth is no longer maintained.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

Java 17.0.6+10 build and test integration

Process completed with exit code 1.

Java 17.0.6+10 test on docker variantcalling

Process completed with exit code 1.

Java 17.0.6+10 test on docker variantcalling

The v0 series of google-github-actions/auth is no longer maintained.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

Java 17.0.6+10 test on docker conda

The v0 series of google-github-actions/auth is no longer maintained.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

Java 17.0.6+10 test on docker 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The v0 series of google-github-actions/auth is no longer maintained.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

Java 17.0.6+10 test on docker integration

Process completed with exit code 1.

Java 17.0.6+10 build and test unit

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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

Java 17.0.6+10 test on docker unit

Process completed with exit code 1.

Java 17.0.6+10 test on docker 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

Validate script WDLs using womtools

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Validate generated WDLs using womtools

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 build and test cloud

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_CNN_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_M2_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

build and push gatk docker to artifacts

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, docker/metadata-action@v4, docker/setup-buildx-action@v2, docker/build-push-action@v4, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_CNV_SOMATIC_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 build and test integration

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 test on docker variantcalling

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 test on docker conda

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 test on docker integration

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 build and test unit

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Java 17.0.6+10 test on docker unit

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Artifacts

Produced during runtime

Name	Size
gatkDockerImage Expired	2.34 GB
test-results-17.0.6+10-cloud Expired	293 KB
test-results-17.0.6+10-integration Expired	3.56 MB
test-results-17.0.6+10-unit Expired	154 MB
test-results-docker-17.0.6+10-conda Expired	316 KB
test-results-docker-17.0.6+10-integration Expired	3.48 MB
test-results-docker-17.0.6+10-unit Expired	153 MB
test-results-docker-17.0.6+10-variantcalling Expired	261 KB