VS-1009 Add SCORE to VQSR Lite VCF #2829
gbggrantgatk-tests.yml
on: pull_request
check if the environment has privileges
1s
build and push gatk docker to artifacts
20m 19s
Validate script WDLs using womtools
3m 57s
Validate generated WDLs using womtools
13m 44s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
10 errors and 55 warnings
|
Java 8 test on docker unit
Process completed with exit code 1.
|
|
Java 8 test on docker unit
Stream Closed
|
|
Java 8 test on docker unit
Process completed with exit code 1.
|
|
Java 8 test on docker integration
No space left on device : '/home/runner/runners/2.306.0/_diag/pages/1b92149f-f3a9-44b9-8635-087f60a324c7_a5fa21b6-8fd8-561a-183e-bf5f6f8b2876_1.log'
|
|
Java 8 test on docker integration
No space left on device : '/home/runner/runners/2.306.0/_diag/pages/1b92149f-f3a9-44b9-8635-087f60a324c7_ecdbf8e8-0e75-58f1-7acf-80c06806a8e2_1.log'
|
|
Java 8 test on docker integration
No space left on device : '/home/runner/work/_actions/actions/upload-artifact/v2'
|
|
Java 8 test on docker conda
Process completed with exit code 1.
|
|
Java 8 test on docker conda
No space left on device
|
|
Java 8 test on docker conda
Process completed with exit code 1.
|
|
Java 8 test on docker variantcalling
System.IO.IOException: No space left on device : '/home/runner/runners/2.306.0/_diag/Worker_20230720-233552-utc.log'
at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset)
at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite()
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)
|
|
check if the environment has privileges
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Validate script WDLs using womtools
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Validate script WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
|
|
Validate script WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
|
|
Validate generated WDLs using womtools
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Validate generated WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
|
|
Validate generated WDLs using womtools
Unexpected input(s) 'fetch', valid inputs are ['repository', 'ref', 'token', 'ssh-key', 'ssh-known-hosts', 'ssh-strict', 'persist-credentials', 'path', 'clean', 'fetch-depth', 'lfs', 'submodules', 'set-safe-directory']
|
|
build and push gatk docker to artifacts
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38, docker/setup-buildx-action@v1, docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
build and push gatk docker to artifacts
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
WDL test RUN_CNN_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 11 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test cloud
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test unit
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test unit
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 test on docker unit
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
|
|
Java 8 test on docker unit
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 test on docker unit
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 0 MB
|
|
Java 8 test on docker integration
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
WDL test RUN_M2_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 test on docker conda
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
|
|
Java 8 test on docker conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/download-artifact@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 test on docker variantcalling
You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 50 MB
|
|
WDL test RUN_CNV_SOMATIC_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 build and test cloud
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 8 build and test cloud
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
Java 11 build and test integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test integration
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
|
Java 11 build and test integration
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-java@v2, actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
|
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-java@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
Artifacts
Produced during runtime
| Name | Size | |
|---|---|---|
|
gatkDockerImage
Expired
|
2.27 GB |
|
|
test-results-11-cloud
Expired
|
250 KB |
|
|
test-results-11-integration
Expired
|
4.49 MB |
|
|
test-results-11-unit
Expired
|
63 MB |
|
|
test-results-8-cloud
Expired
|
250 KB |
|