Changed flow allele filtering in Mutect2 to work separately on the tumor and the normal samples #5990
ilyasoifergatk-tests.yml
on: pull_request
check if the environment has privileges
2s
build and push gatk docker to artifacts
13m 7s
Validate script WDLs using womtools
1m 20s
Validate generated WDLs using womtools
14m 59s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
5 errors and 2 warnings
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251222-093100-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_20251222-093100-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_20251222-093100-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)
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251222-093100-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_20251222-093100-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_20251222-093100-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)
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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_20251222-093101-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_20251222-093101-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_20251222-093101-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)
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conda test on docker Java 17.0.6+10
Process completed with exit code 1.
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variantcalling test on docker Java 17.0.6+10
Process completed with exit code 1.
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cloud build and test Java 17.0.6+10
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
Error: Path Validation Error: Path(s) specified in the action for caching do(es) not exist, hence no cache is being saved.
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Artifacts
Produced during runtime
| Name | Size | Digest | |
|---|---|---|---|
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gatkDockerImage
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2.29 GB |
sha256:0a1bae179e7f74bf7df52e89a8476b4283665717fdf2a57dbd74bc2853da8193
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test-results-17.0.6+10-integration
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583 KB |
sha256:31fee5665ad70cf20fcc2fb931fa617a4717f9085156b2048cb61a9bfed042d0
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test-results-17.0.6+10-unit
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5.06 MB |
sha256:5a91623965276913911cb9019880c3541271b01c931b345b442c01ff5d7b80ff
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test-results-docker-17.0.6+10-conda
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61 KB |
sha256:533b5b5a3fb036644f795cd1f743dcf26f6928dd7a2a1a9782a005e61cc78c20
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test-results-docker-17.0.6+10-integration
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586 KB |
sha256:646ed20f7425dda431476a331f2deeb5b54b49c87b201fc89c8c64823799b2fb
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test-results-docker-17.0.6+10-unit
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4.93 MB |
sha256:28179701c91549f1b406acb9ca79de4cfd906ba4f1d2ba9111873008f9ccd14d
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test-results-docker-17.0.6+10-variantcalling
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119 KB |
sha256:9b2844d8b030857012fa83e1da3bf559a7575b7cb7d5b29009c14e34f8db65fe
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