Skip to content
Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5965

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] #5965

Triggered via pull request December 6, 2025 22:48
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 45m 34s
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 28s
build and push gatk docker to artifacts
Validate script WDLs using womtools
2m 53s
Validate script WDLs using womtools
Validate generated WDLs using womtools
14m 37s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Fit to window
Zoom out
Zoom in

Annotations

12 errors
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.
WDL test RUN_CNV_SOMATIC_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_20251206-224827-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_20251206-224827-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_20251206-224827-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)
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
Process completed with exit code 1.
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
sha256:7c99436fe25b9fa8f8e5126fe6d963115bf5934690948a6dc154c4f6a5fdf32d
test-results-17.0.6+10-cloud
86.9 KB
sha256:eb4f23842fafbd82b5e269e558aaa11283e1a55c2b9327eff1c5c25ea709e51e
test-results-17.0.6+10-integration
577 KB
sha256:05e9cf98abea2cf34559142f978411db9b9adf617eb0fe9f895a25c31a3d23f3
test-results-17.0.6+10-unit
5.15 MB
sha256:566a8d1818cdec362101464b854b296c0ce6c6b7daabdd5e5662b9c9c4b8ce37
test-results-docker-17.0.6+10-conda
59.6 KB
sha256:6b01d2b8fc77a85551001a287344f36aad9c6947364cd0be35c09ef647f4d562
test-results-docker-17.0.6+10-integration
580 KB
sha256:1f08943145356c6eae6f536aa0b2314db2d99abbd9064d11c6f7931119a6a7ba
test-results-docker-17.0.6+10-unit
5 MB
sha256:7bc125558e68b483948cc60978e9734d7905ead1cb7086c1f4a7714732ae41b3
test-results-docker-17.0.6+10-variantcalling
31.8 KB
sha256:d1c03a855c144c390ba08db0a793f29a37e36c15b18bb455c00763ce7bd856a5