Class org.broadinstitute.hellbender.utils.spark.SparkUtilsUnitTest

20

tests

0

failures

0

ignored

6.517s

duration

100%

successful

Tests

Test Duration Result
testConvertHeaderlessHadoopBamShardToBam 0.004s passed
testInvalidSort 1.387s passed
testPathExists 1.905s passed
testPutReadsWithSameNameInSamePartition[0](1, 1, 2, [I@786ee9d5) 0.633s passed
testPutReadsWithSameNameInSamePartition[10](20, 7, 5, [I@761d21b) 0.061s passed
testPutReadsWithSameNameInSamePartition[1](2, 2, 2, [I@75f9539a) 0.076s passed
testPutReadsWithSameNameInSamePartition[2](3, 2, 2, [I@58f73dfb) 0.078s passed
testPutReadsWithSameNameInSamePartition[3](3, 3, 2, [I@647e8f85) 0.070s passed
testPutReadsWithSameNameInSamePartition[4](6, 2, 2, [I@66ebe0d2) 0.065s passed
testPutReadsWithSameNameInSamePartition[5](6, 3, 2, [I@3a28afd6) 0.068s passed
testPutReadsWithSameNameInSamePartition[6](6, 4, 2, [I@211b7f6c) 0.054s passed
testPutReadsWithSameNameInSamePartition[7](2, 2, 3, [I@78110383) 0.047s passed
testPutReadsWithSameNameInSamePartition[8](3, 2, 10, [I@536ce294) 0.044s passed
testPutReadsWithSameNameInSamePartition[9](6, 4, 3, [I@19c682ee) 0.049s passed
testReadsMustBeQueryGroupedToFixPartitions 0.002s passed
testReadsPairsSpanningMultiplePartitions 0.388s passed
testSortCoordinateSortMatchesHtsjdk 0.606s passed
testSortQuerynameFixesPartitionBoundaries 0.295s passed
testSortQuerynameSortMatchesHtsjdk 0.625s passed
testSortUsingElementsAsKeys 0.060s passed

Standard error

20:46:06.956 WARN  NativeCodeLoader - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20:46:08.593 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
20:46:08.717 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
20:46:08.721 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:46:08.791 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
20:46:09.142 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:46:09.225 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
20:46:09.226 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:46:09.330 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
20:46:09.367 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:46:09.599 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage18203545216312997496/data/data2/current/BP-551507284-10.1.0.111-1752612368397/current, will proceed with Du for space computation calculation, 
20:46:09.599 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage18203545216312997496/data/data1/current/BP-551507284-10.1.0.111-1752612368397/current, will proceed with Du for space computation calculation, 
20:46:09.635 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
20:46:09.823 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:46:09.823 ERROR DataNode - Command processor encountered interrupt and exit.
20:46:09.824 WARN  DataNode - Ending block pool service for: Block pool BP-551507284-10.1.0.111-1752612368397 (Datanode Uuid b41c0279-4a1a-48c1-87b6-e248f9d9592a) service to localhost/127.0.0.1:37305
20:46:09.824 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:46:09.824 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
20:46:09.825 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
20:46:09.825 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted