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

all > org.broadinstitute.hellbender.utils.spark > SparkUtilsUnitTest
20

tests
0

failures
0

ignored
6.526s

duration
100%

successful

Tests

Test Duration Result
testConvertHeaderlessHadoopBamShardToBam 0.005s passed
testInvalidSort 1.451s passed
testPathExists 1.974s passed
testPutReadsWithSameNameInSamePartition[0](1, 1, 2, [I@332e21b2) 0.746s passed
testPutReadsWithSameNameInSamePartition[10](20, 7, 5, [I@266340c2) 0.059s passed
testPutReadsWithSameNameInSamePartition[1](2, 2, 2, [I@39c1d78a) 0.095s passed
testPutReadsWithSameNameInSamePartition[2](3, 2, 2, [I@29cc4fe6) 0.061s passed
testPutReadsWithSameNameInSamePartition[3](3, 3, 2, [I@1878ccbd) 0.072s passed
testPutReadsWithSameNameInSamePartition[4](6, 2, 2, [I@7eb3dd4f) 0.066s passed
testPutReadsWithSameNameInSamePartition[5](6, 3, 2, [I@6be6dda0) 0.053s passed
testPutReadsWithSameNameInSamePartition[6](6, 4, 2, [I@d3c8358) 0.053s passed
testPutReadsWithSameNameInSamePartition[7](2, 2, 3, [I@4efa3898) 0.042s passed
testPutReadsWithSameNameInSamePartition[8](3, 2, 10, [I@37a2676) 0.044s passed
testPutReadsWithSameNameInSamePartition[9](6, 4, 3, [I@459ebce) 0.047s passed
testReadsMustBeQueryGroupedToFixPartitions 0.002s passed
testReadsPairsSpanningMultiplePartitions 0.359s passed
testSortCoordinateSortMatchesHtsjdk 0.467s passed
testSortQuerynameFixesPartitionBoundaries 0.243s passed
testSortQuerynameSortMatchesHtsjdk 0.632s passed
testSortUsingElementsAsKeys 0.055s passed

Standard error

15:04:31.869 WARN  NativeCodeLoader - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15:04:33.535 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
15:04:33.663 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
15:04:33.667 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:04:33.739 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
15:04:34.097 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:04:34.184 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
15:04:34.185 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:04:34.285 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
15:04:34.326 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:04:34.571 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2013442606284831256/data/data2/current/BP-1740565577-10.1.0.125-1772636673291/current, will proceed with Du for space computation calculation, 
15:04:34.571 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2013442606284831256/data/data1/current/BP-1740565577-10.1.0.125-1772636673291/current, will proceed with Du for space computation calculation, 
15:04:34.626 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
15:04:34.821 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
15:04:34.821 ERROR DataNode - Command processor encountered interrupt and exit.
15:04:34.822 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
15:04:34.822 WARN  DataNode - Ending block pool service for: Block pool BP-1740565577-10.1.0.125-1772636673291 (Datanode Uuid 46487619-014b-445f-95cb-53d29a7e6258) service to localhost/127.0.0.1:42445
15:04:34.822 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
15:04:34.823 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
15:04:34.823 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted