Skip to content
Build and Test GATK 4

Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767] #5956

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] #5956

Triggered via pull request December 5, 2025 16:34
@mcovarrmcovarr
synchronize #9299
vs_1520_loftee
Status Success
Total duration 47m 5s
Artifacts 8

gatk-tests.yml

on: pull_request
check if the environment has privileges
4s
check if the environment has privileges
build and push gatk docker to artifacts
12m 46s
build and push gatk docker to artifacts
Validate script WDLs using womtools
3m 17s
Validate script WDLs using womtools
Validate generated WDLs using womtools
15m 5s
Validate generated WDLs using womtools
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Fit to window
Zoom out
Zoom in

Annotations

10 errors
WDL test RUN_CNV_SOMATIC_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_M2_WDL on cromwell
System.IO.IOException: No space left on device : '/home/runner/actions-runner/cached/_diag/Worker_20251205-163434-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_20251205-163434-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_20251205-163434-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:e1ecd37bb8674804bd995fefe3bdc1c57eea401d9a32165897709f62741f7ed1
test-results-17.0.6+10-cloud
86.9 KB
sha256:1130d40102d400d6de1413c6e5859eaabd18a0c340d02387b6d5dac86a949d48
test-results-17.0.6+10-integration
578 KB
sha256:8edc25680a227e86a3618c2c64a0fa3022dc369d61431826afe1bd3a75a6bd0a
test-results-17.0.6+10-unit
5.15 MB
sha256:9f509bf4e798390bb3606d7dc77d023a2162470fda7da42c1bb0ff0368346029
test-results-docker-17.0.6+10-conda
59.5 KB
sha256:40e082e188debe5adb6be13829ab75d0e4bbc256a31beb43993da4821112cd0b
test-results-docker-17.0.6+10-integration
581 KB
sha256:e990f604852d4678bde52de32961fbe7acf222fe064be9908ff68fe4c0f48485
test-results-docker-17.0.6+10-unit
5.01 MB
sha256:babba9b23eecb5e46d9b1f9df29acef18486b7ef4067ea2adc95e6b7d0785257
test-results-docker-17.0.6+10-variantcalling
31.9 KB
sha256:7da01821b4ea603819888c8abbc2d620a216530891032497285dee14a1f0b454