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Build and Test GATK 4

test new htsjdk #3558

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test new htsjdk

test new htsjdk #3558

Triggered via pull request December 13, 2023 17:50
@lbergelsonlbergelson
synchronize #8620
lb_run_tests_against_htsjdk
Status Failure
Total duration 33m 36s
Artifacts 3

gatk-tests.yml

on: pull_request
check if the environment has privileges
0s
check if the environment has privileges
build and push gatk docker to artifacts
7m 0s
build and push gatk docker to artifacts
Validate script WDLs using womtools
1m 53s
Validate script WDLs using womtools
Validate generated WDLs using womtools
13m 55s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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7 errors and 6 warnings
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
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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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 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The v0 series of google-github-actions/auth is no longer maintained.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
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_CNN_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_M2_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_CNV_SOMATIC_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.

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