Build and Test GATK 4

Update the GATK base image to a newer LTS ubuntu release #3520

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Triggered via pull request December 9, 2023 19:26

droazen

synchronize #8610

dr_update_docker_base_image

Status Failure

Total duration 32m 17s

Artifacts 3

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

13 errors

build and push gatk docker to artifacts

buildx failed with: ERROR: failed to solve: process "/bin/sh -c conda env create -n gatk -f /gatk/gatkcondaenv.yml && echo \"source activate gatk\" >> /gatk/gatkenv.rc && echo \"source /gatk/gatk-completion.sh\" >> /gatk/gatkenv.rc && conda clean -afy && rm -rf /root/.cache/pip" did not complete successfully: exit code: 1

WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNN_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_SOMATIC_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_M2_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

Process completed with exit code 1.

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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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

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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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

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The v0 series of google-github-actions/auth is no longer maintained.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

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

Artifacts

Produced during runtime

Name	Size
test-results-17.0.6+10-cloud Expired	294 KB
test-results-17.0.6+10-integration Expired	3.57 MB
test-results-17.0.6+10-unit Expired	152 MB