Class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest
|
98%
successful |
Failed tests
testReadAndWriteCRAMAndReferenceOnHDFS
org.apache.hadoop.ipc.RemoteException(java.lang.NoClassDefFoundError): Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java) at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java) at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) at java.base/javax.security.auth.Subject.doAs(Subject.java:439) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) at app//org.apache.hadoop.ipc.Client.getRpcResponse(Client.java:1584) at app//org.apache.hadoop.ipc.Client.call(Client.java:1529) at app//org.apache.hadoop.ipc.Client.call(Client.java:1426) at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:258) at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:139) at app/jdk.proxy3/jdk.proxy3.$Proxy80.getDatanodeReport(Unknown Source) at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.lambda$getDatanodeReport$28(ClientNamenodeProtocolTranslatorPB.java:713) at app//org.apache.hadoop.ipc.internal.ShadedProtobufHelper.ipc(ShadedProtobufHelper.java:160) at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getDatanodeReport(ClientNamenodeProtocolTranslatorPB.java:713) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:437) at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeMethod(RetryInvocationHandler.java:170) at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invoke(RetryInvocationHandler.java:162) at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeOnce(RetryInvocationHandler.java:100) at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:366) at app/jdk.proxy3/jdk.proxy3.$Proxy81.getDatanodeReport(Unknown Source) at app//org.apache.hadoop.hdfs.DFSClient.datanodeReport(DFSClient.java:2134) at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2869) at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2920) at app//org.apache.hadoop.hdfs.MiniDFSCluster.startDataNodes(MiniDFSCluster.java:1848) at app//org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:995) at app//org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:594) at app//org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:533) at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30) at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38) at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.runOnIsolatedMiniCluster(MiniClusterUtils.java:74) at app//org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest.testReadAndWriteCRAMAndReferenceOnHDFS(PrintReadsSparkIntegrationTest.java:88) 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 app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) 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 |
|---|---|---|
| testCoordinateSortedInRegion | 2.496s | passed |
| testFileToFile[0](print_reads.sam, .sam, null) | 0.394s | passed |
| testFileToFile[10](print_reads.sorted.sam, .bam, null) | 0.222s | passed |
| testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.212s | passed |
| testFileToFile[12](print_reads.sorted.bam, .sam, null) | 0.274s | passed |
| testFileToFile[13](print_reads.sorted.bam, .bam, null) | 0.312s | passed |
| testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.292s | passed |
| testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.239s | passed |
| testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.279s | passed |
| testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.265s | passed |
| testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) | 0.186s | passed |
| testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) | 0.202s | passed |
| testFileToFile[1](print_reads.sam, .bam, null) | 0.354s | passed |
| testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.204s | passed |
| testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) | 0.376s | passed |
| testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) | 0.379s | passed |
| testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.381s | passed |
| testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.319s | passed |
| testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.341s | passed |
| testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.335s | passed |
| testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.411s | passed |
| testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.354s | passed |
| testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) | 0.352s | passed |
| testFileToFile[3](print_reads.bam, .sam, null) | 0.463s | passed |
| testFileToFile[4](print_reads.bam, .bam, null) | 0.507s | passed |
| testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) | 0.445s | passed |
| testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) | 0.432s | passed |
| testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) | 0.364s | passed |
| testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) | 0.353s | passed |
| testFileToFile[9](print_reads.sorted.sam, .sam, null) | 0.194s | passed |
| testNonExistentReference | 0.094s | passed |
| testReadAndWriteCRAMAndReferenceOnHDFS | 1.564s | failed |
| testReadFiltering | 0.200s | passed |
| testReadFiltering_asIntegrationTestSpec | 0.203s | passed |
| testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) | 0.191s | 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) | 0.263s | 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) | 0.233s | passed |
| testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.183s | passed |
| testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) | 0.166s | passed |
| testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.173s | passed |
| testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.163s | passed |
| testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) | 0.179s | passed |
| testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) | 0.164s | 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) | 0.163s | passed |
| testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.265s | passed |
| testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.253s | passed |
| testReadThatConsumesNoReferenceBases | 0.274s | passed |
| testSBIIndexGranularityArgument[0](1) | 0.498s | passed |
| testSBIIndexGranularityArgument[1](100) | 0.431s | passed |
| testSequenceDictionaryValidation | 0.090s | passed |
| testUnSorted | 0.264s | passed |
| testUnSortedRoundTrip | 0.212s | 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]) | 0.282s | 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]) | 0.462s | 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]) | 0.445s | 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]) | 0.290s | 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]) | 0.270s | 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]) | 0.278s | 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]) | 0.277s | 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]) | 0.291s | 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]) | 0.287s | 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]) | 0.274s | 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]) | 0.278s | 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]) | 0.389s | passed |
Standard output
-------------------------------------------------------------------------------- [22:43:54] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec
Standard error
[March 28, 2025 at 10:43:44 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:44 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:45 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:45 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:45 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:46 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:46 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:47 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:47 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:47 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:48 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:48 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:48 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:48 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:49 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:49 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:49 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:50 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:50 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:50 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:50 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:50 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:51 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:51 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:52 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:52 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:52 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:52 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:53 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:53 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:53 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:54 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:55 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:55 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:55 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:55 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:55 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:56 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:56 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:56 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:56 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:57 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:58 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:58 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:58 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:58 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:59 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:59 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:43:59 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:44:00 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:44:00 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [March 28, 2025 at 10:44:00 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1096810496 [March 28, 2025 at 10:44:01 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1096810496 22:44:02.925 ERROR DataNode - Initialization failed for Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:39705. Exiting. java.io.IOException: DN shut down before block pool connected at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.retrieveNamespaceInfo(BPServiceActor.java:276) ~[hadoop-hdfs-3.4.0.jar:?] at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.connectToNNAndHandshake(BPServiceActor.java:306) ~[hadoop-hdfs-3.4.0.jar:?] at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.run(BPServiceActor.java:889) [hadoop-hdfs-3.4.0.jar:?] at java.base/java.lang.Thread.run(Thread.java:833) [?:?] 22:44:02.927 ERROR DataNode - Command processor encountered interrupt and exit. [March 28, 2025 at 10:44:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1096810496 [March 28, 2025 at 10:44:03 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1096810496 [March 28, 2025 at 10:44:04 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1096810496