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Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF. [VS-1609] #5090

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Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF. [VS-1609]

Addressed an edge case in ScoreVariantAnnotations that can occur when one variant type is not present in the input VCF. [VS-1609] #5090

Triggered via pull request March 5, 2025 21:43
@mcovarrmcovarr
opened #9113
vs_1609_edge_case
Status Success
Total duration 4h 37m 17s
Artifacts 8

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
3h 23m
build and push gatk docker to artifacts
Validate script WDLs using womtools
1m 3s
Validate script WDLs using womtools
Validate generated WDLs using womtools
13m 14s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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Annotations

15 errors and 9 warnings
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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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The v0 series of google-github-actions/setup-gcloud is no longer maintained.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The v0 series of google-github-actions/auth is no longer maintained.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_CNN_WDL on cromwell
Process completed with exit code 1.
Java 17.0.6+10 test on docker 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 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
Java 17.0.6+10 test on docker conda
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 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 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 variantcalling
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 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
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
Validate script WDLs using womtools
Cache not found for keys: setup-java-Linux-x64-gradle-ba62d0449bc5244dfc3bf0ed00ad0eef42547f190650bbecf54f52acbf26a4a0
Validate generated WDLs using womtools
Cache not found for keys: setup-java-Linux-x64-gradle-ba62d0449bc5244dfc3bf0ed00ad0eef42547f190650bbecf54f52acbf26a4a0
Validate generated WDLs using womtools
Failed to save: Failed to CreateCacheEntry: Received non-retryable error: Failed request: (409) Conflict: cache entry with the same key, version, and scope already exists
Java 17.0.6+10 build and test unit
Cache not found for keys: setup-java-Linux-x64-gradle-ba62d0449bc5244dfc3bf0ed00ad0eef42547f190650bbecf54f52acbf26a4a0
Java 17.0.6+10 build and test unit
Failed to save: Failed to CreateCacheEntry: Received non-retryable error: Failed request: (409) Conflict: cache entry with the same key, version, and scope already exists
Java 17.0.6+10 build and test cloud
Cache not found for keys: setup-java-Linux-x64-gradle-ba62d0449bc5244dfc3bf0ed00ad0eef42547f190650bbecf54f52acbf26a4a0
Java 17.0.6+10 build and test cloud
Failed to save: Failed to CreateCacheEntry: Received non-retryable error: Failed request: (409) Conflict: cache entry with the same key, version, and scope already exists
Java 17.0.6+10 build and test integration
Failed to save: Failed to CreateCacheEntry: Received non-retryable error: Failed request: (409) Conflict: cache entry with the same key, version, and scope already exists
Java 17.0.6+10 build and test integration
Cache not found for keys: setup-java-Linux-x64-gradle-ba62d0449bc5244dfc3bf0ed00ad0eef42547f190650bbecf54f52acbf26a4a0

Artifacts

Produced during runtime
Name Size
gatkDockerImage
2.24 GB
test-results-17.0.6+10-cloud
95.1 KB
test-results-17.0.6+10-integration
567 KB
test-results-17.0.6+10-unit
12 MB
test-results-docker-17.0.6+10-conda
55.8 KB
test-results-docker-17.0.6+10-integration
568 KB
test-results-docker-17.0.6+10-unit
11.9 MB
test-results-docker-17.0.6+10-variantcalling
31.3 KB