[DO NOT MERGE] #4952
jamesemerygatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
28m 54s
Validate script WDLs using womtools
51s
Validate generated WDLs using womtools
14m 3s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
16 errors and 22 warnings
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
Process completed with exit code 1.
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WDL test RUN_M2_WDL on cromwell
Process completed with exit code 1.
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Java 17.0.6+10 build and test cloud
The v0 series of google-github-actions/auth is no longer maintained.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
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Java 17.0.6+10 build and test unit
The v0 series of google-github-actions/auth is no longer maintained.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
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Java 17.0.6+10 build and test integration
The v0 series of google-github-actions/auth is no longer maintained.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
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Java 17.0.6+10 test on docker unit
Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20241210-193651-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)
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20241210-193651-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/runners/2.321.0/_diag/Worker_20241210-193651-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)
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Java 17.0.6+10 test on docker unit
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
|
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Java 17.0.6+10 test on docker integration
Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20241210-193652-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)
System.IO.IOException: No space left on device : '/home/runner/runners/2.321.0/_diag/Worker_20241210-193652-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/runners/2.321.0/_diag/Worker_20241210-193652-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)
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Java 17.0.6+10 test on docker integration
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
|
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Java 17.0.6+10 test on docker variantcalling
Process completed with exit code 1.
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Java 17.0.6+10 test on docker variantcalling
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
|
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Java 17.0.6+10 test on docker conda
Process completed with exit code 1.
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Java 17.0.6+10 test on docker conda
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
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check if the environment has privileges
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Validate script WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 85 MB
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 68 MB
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 46 MB
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WDL test RUN_M2_WDL on cromwell
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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WDL test RUN_M2_WDL on cromwell
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 49 MB
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Validate generated WDLs using womtools
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 build and test cloud
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Java 17.0.6+10 build and test unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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build and push gatk docker to artifacts
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Java 17.0.6+10 build and test integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker unit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker integration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Java 17.0.6+10 test on docker integration
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 98 MB
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Java 17.0.6+10 test on docker variantcalling
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Deprecation notice: v1, v2, and v3 of the artifact actions
The following artifacts were uploaded using a version of actions/upload-artifact that is scheduled for deprecation: "gatkDockerImage", "test-results-17.0.6+10-cloud", "test-results-17.0.6+10-integration", "test-results-17.0.6+10-unit", "test-results-docker-17.0.6+10-conda", "test-results-docker-17.0.6+10-variantcalling".
Please update your workflow to use v4 of the artifact actions.
Learn more: https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/
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Java 17.0.6+10 test on docker conda
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
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gatkDockerImage
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4.72 GB |
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test-results-17.0.6+10-cloud
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268 KB |
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test-results-17.0.6+10-integration
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3.53 MB |
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test-results-17.0.6+10-unit
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86.3 MB |
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test-results-docker-17.0.6+10-conda
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277 KB |
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test-results-docker-17.0.6+10-variantcalling
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135 KB |
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