Skip to content
Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5954

Sign in to view logs

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] #5954

Triggered via pull request December 5, 2025 10:39
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 46m 3s
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 2s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 49s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 47s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Fit to window
Zoom out
Zoom in

Annotations

11 errors
WDL test RUN_CNV_GERMLINE_COHORT_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_20251205-103906-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_20251205-103906-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_20251205-103906-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.
WDL test RUN_CNV_GERMLINE_CASE_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
sha256:6d17dd621fa24bf2e604cea2babfa11f676c712db3e7c15ae47d8982b854585a
test-results-17.0.6+10-cloud
86.9 KB
sha256:c87df1e48c926b871d6f1042ff36b27fa8dc559eaec42084ac9cdae2fcfd0a87
test-results-17.0.6+10-integration
577 KB
sha256:eb814a9b0b8381485410afb6c783f2588853f31a46a290c571ba2caae6c88cb9
test-results-17.0.6+10-unit
5.15 MB
sha256:078706eaeed761dcb295c48c7fc9fc8c293cadeb12f8abd820bcd20a69b766c5
test-results-docker-17.0.6+10-conda
59.5 KB
sha256:41f05e0e185c535c932ea43d82f34135a7feaeba8dd751277fbbbd9bee1bce58
test-results-docker-17.0.6+10-integration
580 KB
sha256:05d4e0119a14335fed298d0bf63216d66acd8545c5cea19adbfc091e93eb38e4
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:c7dae37b2eb158cd5b4bd8d0ef6ac7cf78a131635d1f4ef2dc296efb1a2c6c94
test-results-docker-17.0.6+10-variantcalling
31.8 KB
sha256:a3e07e102f8a1562218f7d8ab87532a9e57363ae2ca9d71e5ee5d5193c390bdf