Fix some bugs in LeftAlignAndTrimVariants #5989
kachulisgatk-tests.yml
on: pull_request
check if the environment has privileges
4s
build and push gatk docker to artifacts
13m 4s
Validate script WDLs using womtools
1m 26s
Validate generated WDLs using womtools
15m 12s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
11 errors
|
WDL test RUN_CNV_SOMATIC_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.OSFileStreamStrategy.Write(ReadOnlySpan`1 buffer)
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 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_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.OSFileStreamStrategy.Write(ReadOnlySpan`1 buffer)
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 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_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.OSFileStreamStrategy.Write(ReadOnlySpan`1 buffer)
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
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251220-023457-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_20251220-023457-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_20251220-023457-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_CNV_GERMLINE_CASE_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251220-023457-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_20251220-023457-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_20251220-023457-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_CNV_GERMLINE_COHORT_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
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 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_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
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 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_20251220-023457-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
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
|
|
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:c252189b69a194165016df17e5259e233d233abe7e814aea0be6c28c02e61660
|
|
|
test-results-17.0.6+10-cloud
|
82.2 KB |
sha256:e4831aa5d269a73eb99df581749d9142f8414cf41021e46630f3cef8d8b81089
|
|
|
test-results-17.0.6+10-integration
|
583 KB |
sha256:732a4c01bfbfcbf9afc5c4e79b4a78734194b6b428d3f01f8bb38c09b0528c4f
|
|
|
test-results-17.0.6+10-unit
|
5.06 MB |
sha256:9419878be2dedb1e63154675037f12a78d7e0a9f626f7a59ccf78398572285c0
|
|
|
test-results-docker-17.0.6+10-conda
|
52.8 KB |
sha256:bf5bca71b84781e4a0976fe1d566acd8636410285f24182adbb72b82c43571f3
|
|
|
test-results-docker-17.0.6+10-integration
|
585 KB |
sha256:51eb0ef90b0120e82b5308dad6416ae6cfc4b1739d79773e4e520c1b1bf9f22a
|
|
|
test-results-docker-17.0.6+10-unit
|
4.92 MB |
sha256:968a3ecd2440d01b24c94bc793944f69ea268b9d1717f5b26fff23399ba4b0a5
|
|
|
test-results-docker-17.0.6+10-variantcalling
|
31.7 KB |
sha256:b5b78f432183f8591d4118d7a64faccf158842c12a3a5c7f9f55f38430e49886
|
|