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Running Test: Test method testRequirePythonEnvironment(org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest)
Gradle suite > Gradle test > org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest > testRequirePythonEnvironment FAILED
java.lang.NullPointerException: Cannot invoke "Object.getClass()" because the return value of "java.lang.RuntimeException.getCause()" is null
at org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest.testRequirePythonEnvironment(StreamingPythonExecutorIntegrationTest.java:34)
Error messages in another test case:
src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0xE2) for encoding US-ASCII
* <li>Score : A flow-based alignment score. Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
^
src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0x80) for encoding US-ASCII
* <li>Score : A flow-based alignment score. Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
^
src/main/java/org/broadinstitute/hellbender/tools/walkers/groundtruth/GroundTruthScorer.java:68: error: unmappable character (0x99) for encoding US-ASCII
* <li>Score : A flow-based alignment score. Since the alignment is per-flow, in the case that there???s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.</li>
^
This test is skipped without any apparent reason:
Running Test: Test method loadIndex(org.broadinstitute.hellbender.BwaMemIntegrationTest)
Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > loadIndex FAILED
java.lang.UnsatisfiedLinkError: 'boolean org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createReferenceIndex(java.lang.String, java.lang.String, java.lang.String)'
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createReferenceIndex(Native Method)
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createIndexImageFromFastaFile(BwaMemIndex.java:227)
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createIndexImageFromFastaFile(BwaMemIndex.java:196)
at org.broadinstitute.hellbender.BwaMemIntegrationTest.loadIndex(BwaMemIntegrationTest.java:49)
Running Test: Test method testChimericUnpairedMapping(org.broadinstitute.hellbender.BwaMemIntegrationTest)
Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > testChimericUnpairedMapping SKIPPED
Running Test: Test method testPerfectUnpairedMapping(org.broadinstitute.hellbender.BwaMemIntegrationTest)
Gradle suite > Gradle test > org.broadinstitute.hellbender.BwaMemIntegrationTest > testPerfectUnpairedMapping SKIPPED
This test fails because some JAR wasn't built:
Running Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest)
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: No local jar was found, please build one by running
Gradle suite > Gradle test > org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest > testPipeForPicardTools STANDARD_ERROR
No local jar was found, please build one by running
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: /disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar
/disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: or
or
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: export GATK_LOCAL_JAR=<path_to_local_jar>
export GATK_LOCAL_JAR=<path_to_local_jar>
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: No local jar was found, please build one by running
No local jar was found, please build one by running
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err:
Test: Test method testPipeForPicardTools(org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest) produced standard out/err: /disk-samsung/ports/biology/gatk/work/gatk-4.6.0.0/gradlew localJar
etc... etc...
Version: 4.6.0.0
FreeBSD 14.1
The text was updated successfully, but these errors were encountered:
log
Examples of test failures from the above log:
Error messages in another test case:
This test is skipped without any apparent reason:
This test fails because some JAR wasn't built:
etc... etc...
Version: 4.6.0.0
FreeBSD 14.1
The text was updated successfully, but these errors were encountered: