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Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5955

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Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767]

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5955

Triggered via pull request December 5, 2025 12:34
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 44m 54s
Artifacts 8

gatk-tests.yml

on: pull_request
check if the environment has privileges
4s
check if the environment has privileges
build and push gatk docker to artifacts
13m 12s
build and push gatk docker to artifacts
Validate script WDLs using womtools
3m 6s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 55s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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12 errors
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
WDL test RUN_CNV_GERMLINE_CASE_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_M2_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251205-123426-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk) at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251205-123426-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk) at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Common.Tracing.Error(Exception exception) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251205-123426-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.Flush(Boolean flushToDisk) at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at System.Diagnostics.TraceSource.Flush() at GitHub.Runner.Common.Tracing.Dispose(Boolean disposing) at GitHub.Runner.Common.Tracing.Dispose() at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing) at GitHub.Runner.Common.TraceManager.Dispose() at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing) at GitHub.Runner.Common.HostContext.Dispose() at GitHub.Runner.Worker.Program.Main(String[] args)
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 1.
unit build and test Java 17.0.6+10
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
cloud build and test Java 17.0.6+10
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
integration build and test Java 17.0.6+10
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
unit test on docker Java 17.0.6+10
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
conda test on docker Java 17.0.6+10
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
variantcalling test on docker Java 17.0.6+10
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
integration test on docker Java 17.0.6+10
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

Artifacts

Produced during runtime
Name Size Digest
gatkDockerImage
2.29 GB
sha256:3d6724b8b5cb607095297b6ca4602b61b92e9c21e9ab408d4dc7cca8215b654f
test-results-17.0.6+10-cloud
87 KB
sha256:e5eb407bd258679ad569493e7f3fe7d71c9e169b20e36450855d5454cd99d452
test-results-17.0.6+10-integration
577 KB
sha256:8e66bae36b4afc1fa5c2a7c5082f226fa18082e0aa3e440caec8497704228b67
test-results-17.0.6+10-unit
5.15 MB
sha256:225d9aee5ff82d912bee3ee3e34e76f9d17bdf20ab4182bc2fc3a8edd33c6a17
test-results-docker-17.0.6+10-conda
59.4 KB
sha256:9197e43889382b7adb8f1b700b396bbe845d7aa790f883cf308a66d5c6549df3
test-results-docker-17.0.6+10-integration
580 KB
sha256:3732582bd79e22fe680a3085a84f745e4312c7d044f8705e0542479b5101dac5
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:eef03f898bc742b94cf69c75b43ec2ce56aa4a7b55538993c7b17f3aa5965790
test-results-docker-17.0.6+10-variantcalling
31.8 KB
sha256:bf9abe996ed8a842d02ec8c8ff1ef04c41b0b0336d96299cce72b00b5868d95d