Class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pipelines > PrintReadsSparkIntegrationTest

124

tests

failures

ignored

25.105s

duration

98%

successful

Failed tests
Tests
Standard output
Standard error

Failed tests

doFileToFileUsingReferenceBundle

org.testng.TestNGException: 
Cannot inject @Test annotated Method [doFileToFileUsingReferenceBundle] with [class java.lang.String, class java.lang.String, class java.lang.String, boolean].
For more information on native dependency injection please refer to https://testng.org/doc/documentation-main.html#native-dependency-injection
	at app//org.testng.internal.Parameters.checkParameterTypes(Parameters.java:436)
	at app//org.testng.internal.Parameters.createParametersForMethod(Parameters.java:350)
	at app//org.testng.internal.Parameters.createParameters(Parameters.java:693)
	at app//org.testng.internal.Parameters.handleParameters(Parameters.java:879)
	at app//org.testng.internal.Parameters.handleParameters(Parameters.java:728)
	at app//org.testng.internal.invokers.ParameterHandler.handleParameters(ParameterHandler.java:72)
	at app//org.testng.internal.invokers.ParameterHandler.createParameters(ParameterHandler.java:51)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:924)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

Tests

Test	Duration	Result
doFileToFileUsingReferenceBundle	0s	failed
testCoordinateSortedInRegion	2.731s	passed
testFileToFileUsingReferenceBundle[0](print_reads.sam, .sam, null)	0s	passed
testFileToFileUsingReferenceBundle[10](print_reads.sorted.sam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[12](print_reads.sorted.bam, .sam, null)	0s	passed
testFileToFileUsingReferenceBundle[13](print_reads.sorted.bam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null)	0s	passed
testFileToFileUsingReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[1](print_reads.sam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null)	0s	passed
testFileToFileUsingReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[3](print_reads.bam, .sam, null)	0s	passed
testFileToFileUsingReferenceBundle[4](print_reads.bam, .bam, null)	0s	passed
testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileUsingReferenceBundle[9](print_reads.sorted.sam, .sam, null)	0s	passed
testFileToFileWithReferenceBundle[0](print_reads.sam, .sam, null)	-	ignored
testFileToFileWithReferenceBundle[10](print_reads.sorted.sam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[12](print_reads.sorted.bam, .sam, null)	-	ignored
testFileToFileWithReferenceBundle[13](print_reads.sorted.bam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null)	-	ignored
testFileToFileWithReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[1](print_reads.sam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null)	-	ignored
testFileToFileWithReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[3](print_reads.bam, .sam, null)	-	ignored
testFileToFileWithReferenceBundle[4](print_reads.bam, .bam, null)	-	ignored
testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)	-	ignored
testFileToFileWithReferenceBundle[9](print_reads.sorted.sam, .sam, null)	-	ignored
testFileToFile[0](print_reads.sam, .sam, null)	0.348s	passed
testFileToFile[10](print_reads.sorted.sam, .bam, null)	0.208s	passed
testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta)	0.190s	passed
testFileToFile[12](print_reads.sorted.bam, .sam, null)	0.274s	passed
testFileToFile[13](print_reads.sorted.bam, .bam, null)	0.295s	passed
testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta)	0.284s	passed
testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta)	0.253s	passed
testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta)	0.252s	passed
testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta)	0.246s	passed
testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null)	0.196s	passed
testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null)	0.193s	passed
testFileToFile[1](print_reads.sam, .bam, null)	0.369s	passed
testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)	0.191s	passed
testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null)	0.354s	passed
testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null)	0.372s	passed
testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)	0.354s	passed
testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)	0.301s	passed
testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)	0.307s	passed
testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)	0.323s	passed
testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)	0.323s	passed
testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)	0.318s	passed
testFileToFile[2](print_reads.sam, .cram, print_reads.fasta)	0.308s	passed
testFileToFile[3](print_reads.bam, .sam, null)	0.472s	passed
testFileToFile[4](print_reads.bam, .bam, null)	0.452s	passed
testFileToFile[5](print_reads.bam, .cram, print_reads.fasta)	0.475s	passed
testFileToFile[6](print_reads.cram, .sam, print_reads.fasta)	0.411s	passed
testFileToFile[7](print_reads.cram, .bam, print_reads.fasta)	0.359s	passed
testFileToFile[8](print_reads.cram, .cram, print_reads.fasta)	0.393s	passed
testFileToFile[9](print_reads.sorted.sam, .sam, null)	0.186s	passed
testNonExistentReference	0.068s	passed
testReadAndWriteCRAMAndReferenceOnHDFS	5.142s	passed
testReadFiltering	0.182s	passed
testReadFiltering_asIntegrationTestSpec	0.185s	passed
testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7)	0.162s	passed
testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8)	0.258s	passed
testReadFilters[11](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2)	0.240s	passed
testReadFilters[12](print_reads.sorted.cram, print_reads.fasta, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2)	0.211s	passed
testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8)	0.168s	passed
testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8)	0.163s	passed
testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8)	0.170s	passed
testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2)	0.165s	passed
testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8)	0.171s	passed
testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0)	0.157s	passed
testReadFilters[7](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2)	0.157s	passed
testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8)	0.242s	passed
testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2)	0.254s	passed
testReadThatConsumesNoReferenceBases	0.279s	passed
testSBIIndexGranularityArgument[0](1)	0.458s	passed
testSBIIndexGranularityArgument[1](100)	0.367s	passed
testSequenceDictionaryValidation	0.088s	passed
testUnSorted	0.246s	passed
testUnSortedRoundTrip	0.182s	passed
testUnmappedReadInclusion[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [unmapped], [u1, u2, u3, u4, u5])	0.266s	passed
testUnmappedReadInclusion[10](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i])	0.435s	passed
testUnmappedReadInclusion[11](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i])	0.459s	passed
testUnmappedReadInclusion[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals], [u1, u2, u3, u4, u5])	0.277s	passed
testUnmappedReadInclusion[2](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, unmapped], [a, b, c, u1, u2, u3, u4, u5])	0.259s	passed
testUnmappedReadInclusion[3](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, 4:700-701, unmapped], [a, b, c, k, u1, u2, u3, u4, u5])	0.256s	passed
testUnmappedReadInclusion[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals], [a, b, c, k, u1, u2, u3, u4, u5])	0.271s	passed
testUnmappedReadInclusion[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [unmapped], [g, h, h, i, i])	0.270s	passed
testUnmappedReadInclusion[6](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011], [a, b, c, d, e])	0.263s	passed
testUnmappedReadInclusion[7](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i])	0.269s	passed
testUnmappedReadInclusion[8](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i])	0.259s	passed
testUnmappedReadInclusion[9](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [unmapped], [g, h, h, i, i])	0.364s	passed

Standard output

--------------------------------------------------------------------------------
[14:56:27] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec

Standard error

[May 27, 2025 at 2:56:17 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:19 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:19 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:33 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[May 27, 2025 at 2:56:33 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=589299712
[May 27, 2025 at 2:56:34 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 2:56:38 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1153433600
14:56:39.214 ERROR DataNode - Command processor encountered interrupt and exit.
[May 27, 2025 at 2:56:39 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 2:56:40 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 2:56:40 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600