Class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest
|
98%
successful |
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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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 | 2.414s | 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) | 0.001s | 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 |
| testFileToFile[0](print_reads.sam, .sam, null) | 0.384s | passed |
| testFileToFile[10](print_reads.sorted.sam, .bam, null) | 0.224s | passed |
| testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.214s | passed |
| testFileToFile[12](print_reads.sorted.bam, .sam, null) | 0.269s | passed |
| testFileToFile[13](print_reads.sorted.bam, .bam, null) | 0.306s | passed |
| testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.294s | passed |
| testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.267s | passed |
| testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.267s | passed |
| testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.273s | passed |
| testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) | 0.218s | passed |
| testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) | 0.216s | passed |
| testFileToFile[1](print_reads.sam, .bam, null) | 0.313s | passed |
| testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.209s | passed |
| testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) | 0.370s | passed |
| testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) | 0.382s | passed |
| testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.372s | passed |
| testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.324s | passed |
| testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.320s | passed |
| testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.318s | passed |
| testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.334s | passed |
| testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.309s | passed |
| testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) | 0.334s | passed |
| testFileToFile[3](print_reads.bam, .sam, null) | 0.528s | passed |
| testFileToFile[4](print_reads.bam, .bam, null) | 0.547s | passed |
| testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) | 0.471s | passed |
| testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) | 0.434s | passed |
| testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) | 0.440s | passed |
| testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) | 0.374s | passed |
| testFileToFile[9](print_reads.sorted.sam, .sam, null) | 0.222s | passed |
| testNonExistentReference | 0.101s | passed |
| testReadAndWriteCRAMAndReferenceOnHDFS | - | ignored |
| testReadFiltering | 0.199s | passed |
| testReadFiltering_asIntegrationTestSpec | 0.201s | passed |
| testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) | 0.185s | passed |
| testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) | 0.248s | 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) | 0.261s | 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) | 0.240s | passed |
| testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.178s | passed |
| testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) | 0.181s | passed |
| testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.168s | passed |
| testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.172s | passed |
| testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) | 0.176s | passed |
| testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) | 0.175s | 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) | 0.193s | passed |
| testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.271s | passed |
| testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.264s | passed |
| testReadThatConsumesNoReferenceBases | 0.270s | passed |
| testSBIIndexGranularityArgument[0](1) | 0.378s | passed |
| testSBIIndexGranularityArgument[1](100) | 0.359s | passed |
| testSequenceDictionaryValidation | 0.113s | passed |
| testUnSorted | 0.260s | passed |
| testUnSortedRoundTrip | 0.189s | passed |
| testUnmappedReadInclusion[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [unmapped], [u1, u2, u3, u4, u5]) | 0.272s | passed |
| testUnmappedReadInclusion[10](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/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](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/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]) | 0.455s | passed |
| testUnmappedReadInclusion[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals], [u1, u2, u3, u4, u5]) | 0.265s | passed |
| testUnmappedReadInclusion[2](/gatkCloneMountPoint/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]) | 0.270s | passed |
| testUnmappedReadInclusion[3](/gatkCloneMountPoint/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]) | 0.266s | passed |
| testUnmappedReadInclusion[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals], [a, b, c, k, u1, u2, u3, u4, u5]) | 0.267s | passed |
| testUnmappedReadInclusion[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [unmapped], [g, h, h, i, i]) | 0.268s | passed |
| testUnmappedReadInclusion[6](/gatkCloneMountPoint/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]) | 0.271s | passed |
| testUnmappedReadInclusion[7](/gatkCloneMountPoint/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]) | 0.272s | passed |
| testUnmappedReadInclusion[8](/gatkCloneMountPoint/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]) | 0.268s | passed |
| testUnmappedReadInclusion[9](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [unmapped], [g, h, h, i, i]) | 0.364s | passed |
Standard output
-------------------------------------------------------------------------------- [16:48:41] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec
Standard error
[May 27, 2025 at 4:48:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:44 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:45 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:46 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 4:48:47 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=526385152 [May 27, 2025 at 4:48:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=926941184 [May 27, 2025 at 4:48:48 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=926941184 [May 27, 2025 at 4:48:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=926941184 [May 27, 2025 at 4:48:49 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=926941184