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Merge master, fix unrelated VDS-making breakage [VS-1777] #5964

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Merge master, fix unrelated VDS-making breakage [VS-1777]

Merge master, fix unrelated VDS-making breakage [VS-1777] #5964

Triggered via pull request December 6, 2025 10:55
@mcovarrmcovarr
synchronize #9302
vs_1777_build_failure
Status Success
Total duration 44m 37s
Artifacts 8

gatk-tests.yml

on: pull_request
check if the environment has privileges
2s
check if the environment has privileges
build and push gatk docker to artifacts
13m 7s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 51s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 50s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
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12 errors
WDL test RUN_CNV_SOMATIC_WDL on cromwell
Process completed with exit code 1.
WDL test RUN_VCF_SITE_LEVEL_FILTERING_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_CNV_GERMLINE_CASE_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_20251206-105503-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.FileStream.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_20251206-105503-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.FileStream.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_20251206-105503-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.FileStream.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)
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
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
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
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
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
sha256:8f541bdb3d12227b236aa3eb25f6a3fb4ca42714ca9847706d105e9eadf30aac
test-results-17.0.6+10-cloud
86.9 KB
sha256:eaf64060fd53c0be6d074d6db661845313c0c8862f99d65e53ad74392263ef9f
test-results-17.0.6+10-integration
579 KB
sha256:f7572dc475f1a2755b20079682c2f69644900e85bddaaf8e7c16e3ea2efa0f40
test-results-17.0.6+10-unit
5.15 MB
sha256:6593951d42c90847ed4d5a3e84d7919fd3db939e8471a9e3e62a44a8bf985018
test-results-docker-17.0.6+10-conda
59.4 KB
sha256:735c75ae83c04846108c542fa92667dfa66d9d0df3d7cd0ca1700fcf86b4c6a4
test-results-docker-17.0.6+10-integration
582 KB
sha256:e4fbe74823e0cdae4aa469769ef6b73e7c4c99a87fd06e928dd8493e26d3375b
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:e23d448a6dbd34e81985ee0d72f0e784a84919a7169f2d37b99c0aaf94368496
test-results-docker-17.0.6+10-variantcalling
31.9 KB
sha256:a6b6ce95489d3b706ca934f5e73f69610dc613b7dc77adead9ff02fd8e83be0f