Class org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSinkUnitTest

32

tests

0

failures

0

ignored

21.557s

duration

100%

successful

Tests

Test Duration Result
testBrokenGVCFCasesAreDisallowed[0](false, .bcf) 0s passed
testBrokenGVCFCasesAreDisallowed[1](false, .bcf.gz) 0.001s passed
testBrokenGVCFCasesAreDisallowed[2](true, .g.bcf) 0s passed
testBrokenGVCFCasesAreDisallowed[3](true, .g.bcf.gz) 0s passed
testEnableDisableGVCFWriting[0](false, .vcf) 0.184s passed
testEnableDisableGVCFWriting[1](false, .vcf.gz) 0.158s passed
testEnableDisableGVCFWriting[2](true, .g.vcf) 0.155s passed
testEnableDisableGVCFWriting[3](true, .g.vcf.gz) 0.162s passed
testWritingToAnExistingFileHDFS[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 1.291s passed
testWritingToAnExistingFileHDFS[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 2.343s passed
testWritingToAnExistingFileHDFS[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 1.583s passed
testWritingToAnExistingFileHDFS[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 1.909s passed
testWritingToAnExistingFileHDFS[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 0.721s passed
testWritingToAnExistingFileHDFS[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 0.650s passed
testWritingToFileURL[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 0.329s passed
testWritingToFileURL[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 0.248s passed
testWritingToFileURL[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.339s passed
testWritingToFileURL[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 0.308s passed
testWritingToFileURL[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 0.252s passed
testWritingToFileURL[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 0.255s passed
variantsSinkHDFSTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 1.079s passed
variantsSinkHDFSTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 2.259s passed
variantsSinkHDFSTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 1.445s passed
variantsSinkHDFSTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 1.920s passed
variantsSinkHDFSTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 1.445s passed
variantsSinkHDFSTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 1.001s passed
variantsSinkTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 0.233s passed
variantsSinkTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 0.271s passed
variantsSinkTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.223s passed
variantsSinkTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 0.246s passed
variantsSinkTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 0.330s passed
variantsSinkTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 0.217s passed

Standard error

18:46:59.807 INFO  MiniDFSCluster - starting cluster: numNameNodes=1, numDataNodes=1
18:46:59.808 INFO  NameNode - Formatting using clusterid: testClusterID
18:46:59.808 INFO  FSEditLog - Edit logging is async:true
18:46:59.822 INFO  FSNamesystem - KeyProvider: null
18:46:59.822 INFO  FSNamesystem - fsLock is fair: true
18:46:59.822 INFO  FSNamesystem - Detailed lock hold time metrics enabled: false
18:46:59.822 INFO  FSNamesystem - fsOwner                = runner (auth:SIMPLE)
18:46:59.822 INFO  FSNamesystem - supergroup             = supergroup
18:46:59.822 INFO  FSNamesystem - isPermissionEnabled    = true
18:46:59.822 INFO  FSNamesystem - isStoragePolicyEnabled = true
18:46:59.822 INFO  FSNamesystem - HA Enabled: false
18:46:59.822 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
18:46:59.822 INFO  DatanodeManager - dfs.block.invalidate.limit : configured=1000, counted=60, effected=1000
18:46:59.822 INFO  DatanodeManager - dfs.namenode.datanode.registration.ip-hostname-check=true
18:46:59.822 INFO  BlockManager - dfs.namenode.startup.delay.block.deletion.sec is set to 000:00:00:00.000
18:46:59.822 INFO  BlockManager - The block deletion will start around 2025 May 19 18:46:59
18:46:59.822 INFO  GSet - Computing capacity for map BlocksMap
18:46:59.822 INFO  GSet - VM type       = 64-bit
18:46:59.822 INFO  GSet - 2.0% max memory 3.4 GB = 70 MB
18:46:59.822 INFO  GSet - capacity      = 2^23 = 8388608 entries
18:46:59.826 INFO  BlockManager - Storage policy satisfier is disabled
18:46:59.826 INFO  BlockManager - dfs.block.access.token.enable = false
18:46:59.826 INFO  BlockManagerSafeMode - dfs.namenode.safemode.threshold-pct = 0.999
18:46:59.826 INFO  BlockManagerSafeMode - dfs.namenode.safemode.min.datanodes = 0
18:46:59.826 INFO  BlockManagerSafeMode - dfs.namenode.safemode.extension = 0
18:46:59.826 INFO  BlockManager - defaultReplication         = 1
18:46:59.826 INFO  BlockManager - maxReplication             = 512
18:46:59.826 INFO  BlockManager - minReplication             = 1
18:46:59.826 INFO  BlockManager - maxReplicationStreams      = 2
18:46:59.826 INFO  BlockManager - redundancyRecheckInterval  = 3000ms
18:46:59.826 INFO  BlockManager - encryptDataTransfer        = false
18:46:59.826 INFO  BlockManager - maxNumBlocksToLog          = 1000
18:46:59.826 INFO  GSet - Computing capacity for map INodeMap
18:46:59.826 INFO  GSet - VM type       = 64-bit
18:46:59.826 INFO  GSet - 1.0% max memory 3.4 GB = 35 MB
18:46:59.826 INFO  GSet - capacity      = 2^22 = 4194304 entries
18:46:59.829 INFO  FSDirectory - ACLs enabled? true
18:46:59.829 INFO  FSDirectory - POSIX ACL inheritance enabled? true
18:46:59.829 INFO  FSDirectory - XAttrs enabled? true
18:46:59.829 INFO  NameNode - Caching file names occurring more than 10 times
18:46:59.829 INFO  SnapshotManager - Loaded config captureOpenFiles: false, skipCaptureAccessTimeOnlyChange: false, snapshotDiffAllowSnapRootDescendant: true, maxSnapshotLimit: 65536
18:46:59.829 INFO  SnapshotManager - SkipList is disabled
18:46:59.829 INFO  GSet - Computing capacity for map cachedBlocks
18:46:59.829 INFO  GSet - VM type       = 64-bit
18:46:59.829 INFO  GSet - 0.25% max memory 3.4 GB = 8.8 MB
18:46:59.829 INFO  GSet - capacity      = 2^20 = 1048576 entries
18:46:59.829 INFO  TopMetrics - NNTop conf: dfs.namenode.top.window.num.buckets = 10
18:46:59.829 INFO  TopMetrics - NNTop conf: dfs.namenode.top.num.users = 10
18:46:59.829 INFO  TopMetrics - NNTop conf: dfs.namenode.top.windows.minutes = 1,5,25
18:46:59.829 INFO  FSNamesystem - Retry cache on namenode is enabled
18:46:59.829 INFO  FSNamesystem - Retry cache will use 0.03 of total heap and retry cache entry expiry time is 600000 millis
18:46:59.829 INFO  GSet - Computing capacity for map NameNodeRetryCache
18:46:59.829 INFO  GSet - VM type       = 64-bit
18:46:59.829 INFO  GSet - 0.029999999329447746% max memory 3.4 GB = 1.0 MB
18:46:59.829 INFO  GSet - capacity      = 2^17 = 131072 entries
18:46:59.830 INFO  FSImage - Allocated new BlockPoolId: BP-63767602-10.1.0.176-1747680419830
18:46:59.833 INFO  Storage - Storage directory /tmp/minicluster_storage189662454199067357/name-0-1 has been successfully formatted.
18:46:59.835 INFO  Storage - Storage directory /tmp/minicluster_storage189662454199067357/name-0-2 has been successfully formatted.
18:46:59.844 INFO  FSImageFormatProtobuf - Saving image file /tmp/minicluster_storage189662454199067357/name-0-1/current/fsimage.ckpt_0000000000000000000 using no compression
18:46:59.846 INFO  FSImageFormatProtobuf - Saving image file /tmp/minicluster_storage189662454199067357/name-0-2/current/fsimage.ckpt_0000000000000000000 using no compression
18:46:59.847 INFO  FSImageFormatProtobuf - Image file /tmp/minicluster_storage189662454199067357/name-0-1/current/fsimage.ckpt_0000000000000000000 of size 419 bytes saved in 0 seconds .
18:46:59.851 INFO  FSImageFormatProtobuf - Image file /tmp/minicluster_storage189662454199067357/name-0-2/current/fsimage.ckpt_0000000000000000000 of size 419 bytes saved in 0 seconds .
18:46:59.853 INFO  NNStorageRetentionManager - Going to retain 1 images with txid >= 0
18:46:59.857 INFO  FSNamesystem - Stopping services started for active state
18:46:59.857 INFO  FSNamesystem - Stopping services started for standby state
18:46:59.858 INFO  NameNode - createNameNode []
18:46:59.859 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
18:46:59.859 INFO  MetricsSystemImpl - Scheduled Metric snapshot period at 10 second(s).
18:46:59.859 INFO  MetricsSystemImpl - NameNode metrics system started
18:46:59.860 INFO  NameNodeUtils - fs.defaultFS is hdfs://127.0.0.1:0
18:46:59.871 INFO  JvmPauseMonitor - Starting JVM pause monitor
18:46:59.871 INFO  DFSUtil - Filter initializers set : org.apache.hadoop.http.lib.StaticUserWebFilter,org.apache.hadoop.hdfs.web.AuthFilterInitializer
18:46:59.871 INFO  DFSUtil - Starting Web-server for hdfs at: http://localhost:0
18:46:59.872 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
18:46:59.872 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:46:59.873 INFO  HttpServer2 - Added global filter 'safety' (class=org.apache.hadoop.http.HttpServer2$QuotingInputFilter)
18:46:59.873 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context hdfs
18:46:59.873 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context static
18:46:59.874 INFO  HttpServer2 - Added filter AuthFilter (class=org.apache.hadoop.hdfs.web.AuthFilter) to context hdfs
18:46:59.874 INFO  HttpServer2 - Added filter AuthFilter (class=org.apache.hadoop.hdfs.web.AuthFilter) to context static
18:46:59.875 INFO  HttpServer2 - addJerseyResourcePackage: packageName=org.apache.hadoop.hdfs.server.namenode.web.resources;org.apache.hadoop.hdfs.web.resources, pathSpec=/webhdfs/v1/*
18:46:59.875 INFO  HttpServer2 - Jetty bound to port 40289
18:46:59.875 INFO  Server - jetty-9.4.56.v20240826; built: 2024-08-26T17:15:05.868Z; git: ec6782ff5ead824dabdcf47fa98f90a4aedff401; jvm 17.0.6+10
18:46:59.876 INFO  session - DefaultSessionIdManager workerName=node0
18:46:59.876 INFO  session - No SessionScavenger set, using defaults
18:46:59.876 INFO  session - node0 Scavenging every 660000ms
18:46:59.877 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
18:46:59.877 INFO  ContextHandler - Started o.e.j.s.ServletContextHandler@4b5d704{static,/static,jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-hdfs/3.3.6/5058b645375c6a68f509e167ad6a6ada9642df09/hadoop-hdfs-3.3.6-tests.jar!/webapps/static,AVAILABLE}
18:46:59.917 INFO  BlockManagerInfo - Removed broadcast_614_piece0 on localhost:45727 in memory (size: 50.2 KiB, free: 1919.8 MiB)
18:46:59.917 INFO  BlockManagerInfo - Removed broadcast_615_piece0 on localhost:45727 in memory (size: 154.0 KiB, free: 1920.0 MiB)
18:46:59.973 INFO  ContextHandler - Started o.e.j.w.WebAppContext@bef9cd2{hdfs,/,file:///tmp/jetty-localhost-40289-hadoop-hdfs-3_3_6-tests_jar-_-any-9318570872570892617/webapp/,AVAILABLE}{jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-hdfs/3.3.6/5058b645375c6a68f509e167ad6a6ada9642df09/hadoop-hdfs-3.3.6-tests.jar!/webapps/hdfs}
18:46:59.973 INFO  AbstractConnector - Started ServerConnector@7b416f5f{HTTP/1.1, (http/1.1)}{localhost:40289}
18:46:59.974 INFO  Server - Started @78475ms
18:46:59.974 INFO  FSEditLog - Edit logging is async:true
18:46:59.986 INFO  FSNamesystem - KeyProvider: null
18:46:59.986 INFO  FSNamesystem - fsLock is fair: true
18:46:59.986 INFO  FSNamesystem - Detailed lock hold time metrics enabled: false
18:46:59.986 INFO  FSNamesystem - fsOwner                = runner (auth:SIMPLE)
18:46:59.986 INFO  FSNamesystem - supergroup             = supergroup
18:46:59.986 INFO  FSNamesystem - isPermissionEnabled    = true
18:46:59.986 INFO  FSNamesystem - isStoragePolicyEnabled = true
18:46:59.986 INFO  FSNamesystem - HA Enabled: false
18:46:59.986 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
18:46:59.986 INFO  DatanodeManager - dfs.block.invalidate.limit : configured=1000, counted=60, effected=1000
18:46:59.986 INFO  DatanodeManager - dfs.namenode.datanode.registration.ip-hostname-check=true
18:46:59.986 INFO  BlockManager - dfs.namenode.startup.delay.block.deletion.sec is set to 000:00:00:00.000
18:46:59.986 INFO  BlockManager - The block deletion will start around 2025 May 19 18:46:59
18:46:59.986 INFO  GSet - Computing capacity for map BlocksMap
18:46:59.986 INFO  GSet - VM type       = 64-bit
18:46:59.986 INFO  GSet - 2.0% max memory 3.4 GB = 70 MB
18:46:59.986 INFO  GSet - capacity      = 2^23 = 8388608 entries
18:46:59.987 INFO  BlockManager - Storage policy satisfier is disabled
18:46:59.987 INFO  BlockManager - dfs.block.access.token.enable = false
18:46:59.987 INFO  BlockManagerSafeMode - dfs.namenode.safemode.threshold-pct = 0.999
18:46:59.987 INFO  BlockManagerSafeMode - dfs.namenode.safemode.min.datanodes = 0
18:46:59.987 INFO  BlockManagerSafeMode - dfs.namenode.safemode.extension = 0
18:46:59.987 INFO  BlockManager - defaultReplication         = 1
18:46:59.987 INFO  BlockManager - maxReplication             = 512
18:46:59.987 INFO  BlockManager - minReplication             = 1
18:46:59.987 INFO  BlockManager - maxReplicationStreams      = 2
18:46:59.987 INFO  BlockManager - redundancyRecheckInterval  = 3000ms
18:46:59.987 INFO  BlockManager - encryptDataTransfer        = false
18:46:59.987 INFO  BlockManager - maxNumBlocksToLog          = 1000
18:46:59.987 INFO  GSet - Computing capacity for map INodeMap
18:46:59.987 INFO  GSet - VM type       = 64-bit
18:46:59.987 INFO  GSet - 1.0% max memory 3.4 GB = 35 MB
18:46:59.987 INFO  GSet - capacity      = 2^22 = 4194304 entries
18:46:59.988 INFO  FSDirectory - ACLs enabled? true
18:46:59.988 INFO  FSDirectory - POSIX ACL inheritance enabled? true
18:46:59.988 INFO  FSDirectory - XAttrs enabled? true
18:46:59.988 INFO  NameNode - Caching file names occurring more than 10 times
18:46:59.988 INFO  SnapshotManager - Loaded config captureOpenFiles: false, skipCaptureAccessTimeOnlyChange: false, snapshotDiffAllowSnapRootDescendant: true, maxSnapshotLimit: 65536
18:46:59.988 INFO  SnapshotManager - SkipList is disabled
18:46:59.988 INFO  GSet - Computing capacity for map cachedBlocks
18:46:59.988 INFO  GSet - VM type       = 64-bit
18:46:59.988 INFO  GSet - 0.25% max memory 3.4 GB = 8.8 MB
18:46:59.988 INFO  GSet - capacity      = 2^20 = 1048576 entries
18:46:59.988 INFO  TopMetrics - NNTop conf: dfs.namenode.top.window.num.buckets = 10
18:46:59.988 INFO  TopMetrics - NNTop conf: dfs.namenode.top.num.users = 10
18:46:59.988 INFO  TopMetrics - NNTop conf: dfs.namenode.top.windows.minutes = 1,5,25
18:46:59.988 INFO  FSNamesystem - Retry cache on namenode is enabled
18:46:59.988 INFO  FSNamesystem - Retry cache will use 0.03 of total heap and retry cache entry expiry time is 600000 millis
18:46:59.988 INFO  GSet - Computing capacity for map NameNodeRetryCache
18:46:59.988 INFO  GSet - VM type       = 64-bit
18:46:59.989 INFO  GSet - 0.029999999329447746% max memory 3.4 GB = 1.0 MB
18:46:59.989 INFO  GSet - capacity      = 2^17 = 131072 entries
18:46:59.990 INFO  Storage - Lock on /tmp/minicluster_storage189662454199067357/name-0-1/in_use.lock acquired by nodename 3117@pkrvmf6wy0o8zjz
18:46:59.991 INFO  Storage - Lock on /tmp/minicluster_storage189662454199067357/name-0-2/in_use.lock acquired by nodename 3117@pkrvmf6wy0o8zjz
18:46:59.991 INFO  FileJournalManager - Recovering unfinalized segments in /tmp/minicluster_storage189662454199067357/name-0-1/current
18:46:59.991 INFO  FileJournalManager - Recovering unfinalized segments in /tmp/minicluster_storage189662454199067357/name-0-2/current
18:46:59.991 INFO  FSImage - No edit log streams selected.
18:46:59.991 INFO  FSImage - Planning to load image: FSImageFile(file=/tmp/minicluster_storage189662454199067357/name-0-1/current/fsimage_0000000000000000000, cpktTxId=0000000000000000000)
18:46:59.992 INFO  FSImageFormatPBINode - Loading 1 INodes.
18:46:59.992 INFO  FSImageFormatPBINode - Successfully loaded 1 inodes
18:46:59.992 INFO  FSImageFormatPBINode - Completed update blocks map and name cache, total waiting duration 0ms.
18:46:59.992 INFO  FSImageFormatProtobuf - Loaded FSImage in 0 seconds.
18:46:59.992 INFO  FSImage - Loaded image for txid 0 from /tmp/minicluster_storage189662454199067357/name-0-1/current/fsimage_0000000000000000000
18:46:59.992 INFO  FSNamesystem - Need to save fs image? false (staleImage=false, haEnabled=false, isRollingUpgrade=false)
18:46:59.992 INFO  FSEditLog - Starting log segment at 1
18:46:59.996 INFO  NameCache - initialized with 0 entries 0 lookups
18:46:59.996 INFO  FSNamesystem - Finished loading FSImage in 6 msecs
18:46:59.996 INFO  NameNode - RPC server is binding to localhost:0
18:46:59.996 INFO  NameNode - Enable NameNode state context:false
18:46:59.996 INFO  CallQueueManager - Using callQueue: class java.util.concurrent.LinkedBlockingQueue, queueCapacity: 1000, scheduler: class org.apache.hadoop.ipc.DefaultRpcScheduler, ipcBackoff: false.
18:46:59.996 INFO  Server - Listener at localhost:46347
18:46:59.996 INFO  Server - Starting Socket Reader #1 for port 0
18:46:59.998 INFO  NameNode - Clients are to use localhost:46347 to access this namenode/service.
18:46:59.999 INFO  FSNamesystem - Registered FSNamesystemState, ReplicatedBlocksState and ECBlockGroupsState MBeans.
18:47:00.010 INFO  LeaseManager - Number of blocks under construction: 0
18:47:00.010 INFO  DatanodeAdminDefaultMonitor - Initialized the Default Decommission and Maintenance monitor
18:47:00.010 INFO  BlockManager - Start MarkedDeleteBlockScrubber thread
18:47:00.011 INFO  BlockManager - initializing replication queues
18:47:00.011 INFO  StateChange - STATE* Leaving safe mode after 0 secs
18:47:00.011 INFO  StateChange - STATE* Network topology has 0 racks and 0 datanodes
18:47:00.011 INFO  StateChange - STATE* UnderReplicatedBlocks has 0 blocks
18:47:00.015 INFO  Server - IPC Server Responder: starting
18:47:00.015 INFO  BlockManager - Total number of blocks            = 0
18:47:00.015 INFO  Server - IPC Server listener on 0: starting
18:47:00.015 INFO  BlockManager - Number of invalid blocks          = 0
18:47:00.015 INFO  BlockManager - Number of under-replicated blocks = 0
18:47:00.015 INFO  BlockManager - Number of  over-replicated blocks = 0
18:47:00.015 INFO  BlockManager - Number of blocks being written    = 0
18:47:00.015 INFO  StateChange - STATE* Replication Queue initialization scan for invalid, over- and under-replicated blocks completed in 4 msec
18:47:00.016 INFO  NameNode - NameNode RPC up at: localhost/127.0.0.1:46347
18:47:00.016 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:47:00.017 INFO  FSNamesystem - Starting services required for active state
18:47:00.017 INFO  FSDirectory - Initializing quota with 12 thread(s)
18:47:00.017 INFO  FSDirectory - Quota initialization completed in 0 milliseconds
name space=1
storage space=0
storage types=RAM_DISK=0, SSD=0, DISK=0, ARCHIVE=0, PROVIDED=0
18:47:00.018 INFO  CacheReplicationMonitor - Starting CacheReplicationMonitor with interval 30000 milliseconds
18:47:00.018 INFO  MiniDFSCluster - Starting DataNode 0 with dfs.datanode.data.dir: [DISK]file:/tmp/minicluster_storage189662454199067357/data/data1,[DISK]file:/tmp/minicluster_storage189662454199067357/data/data2
18:47:00.019 INFO  ThrottledAsyncChecker - Scheduling a check for [DISK]file:/tmp/minicluster_storage189662454199067357/data/data1
18:47:00.019 INFO  ThrottledAsyncChecker - Scheduling a check for [DISK]file:/tmp/minicluster_storage189662454199067357/data/data2
18:47:00.029 INFO  MetricsSystemImpl - DataNode metrics system started (again)
18:47:00.029 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
18:47:00.029 INFO  BlockScanner - Initialized block scanner with targetBytesPerSec 1048576
18:47:00.029 INFO  DataNode - Configured hostname is 127.0.0.1
18:47:00.029 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
18:47:00.029 INFO  DataNode - Starting DataNode with maxLockedMemory = 0
18:47:00.030 INFO  DataNode - Opened streaming server at /127.0.0.1:36579
18:47:00.030 INFO  DataNode - Balancing bandwidth is 104857600 bytes/s
18:47:00.030 INFO  DataNode - Number threads for balancing is 100
18:47:00.032 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
18:47:00.032 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:47:00.033 INFO  HttpServer2 - Added global filter 'safety' (class=org.apache.hadoop.http.HttpServer2$QuotingInputFilter)
18:47:00.034 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context datanode
18:47:00.034 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context static
18:47:00.034 INFO  HttpServer2 - Jetty bound to port 38355
18:47:00.034 INFO  Server - jetty-9.4.56.v20240826; built: 2024-08-26T17:15:05.868Z; git: ec6782ff5ead824dabdcf47fa98f90a4aedff401; jvm 17.0.6+10
18:47:00.035 INFO  session - DefaultSessionIdManager workerName=node0
18:47:00.035 INFO  session - No SessionScavenger set, using defaults
18:47:00.035 INFO  session - node0 Scavenging every 600000ms
18:47:00.035 INFO  ContextHandler - Started o.e.j.s.ServletContextHandler@2b34746e{static,/static,jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-hdfs/3.3.6/5058b645375c6a68f509e167ad6a6ada9642df09/hadoop-hdfs-3.3.6-tests.jar!/webapps/static,AVAILABLE}
18:47:00.124 INFO  ContextHandler - Started o.e.j.w.WebAppContext@65f36b78{datanode,/,file:///tmp/jetty-localhost-38355-hadoop-hdfs-3_3_6-tests_jar-_-any-916028289655924881/webapp/,AVAILABLE}{jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/org.apache.hadoop/hadoop-hdfs/3.3.6/5058b645375c6a68f509e167ad6a6ada9642df09/hadoop-hdfs-3.3.6-tests.jar!/webapps/datanode}
18:47:00.124 INFO  AbstractConnector - Started ServerConnector@bef9469{HTTP/1.1, (http/1.1)}{localhost:38355}
18:47:00.124 INFO  Server - Started @78625ms
18:47:00.125 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
18:47:00.126 INFO  DatanodeHttpServer - Listening HTTP traffic on /127.0.0.1:33801
18:47:00.126 INFO  DataNode - dnUserName = runner
18:47:00.126 INFO  DataNode - supergroup = supergroup
18:47:00.126 INFO  JvmPauseMonitor - Starting JVM pause monitor
18:47:00.126 INFO  CallQueueManager - Using callQueue: class java.util.concurrent.LinkedBlockingQueue, queueCapacity: 1000, scheduler: class org.apache.hadoop.ipc.DefaultRpcScheduler, ipcBackoff: false.
18:47:00.126 INFO  Server - Listener at localhost:33939
18:47:00.127 INFO  Server - Starting Socket Reader #1 for port 0
18:47:00.128 INFO  DataNode - Opened IPC server at /127.0.0.1:33939
18:47:00.137 INFO  DataNode - Refresh request received for nameservices: null
18:47:00.137 INFO  DataNode - Starting BPOfferServices for nameservices: <default>
18:47:00.138 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:47:00.138 INFO  DataNode - Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:46347 starting to offer service
18:47:00.138 INFO  Server - IPC Server Responder: starting
18:47:00.138 INFO  Server - IPC Server listener on 0: starting
18:47:00.139 INFO  DataNode - Acknowledging ACTIVE Namenode during handshakeBlock pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:46347
18:47:00.140 INFO  Storage - Using 2 threads to upgrade data directories (dfs.datanode.parallel.volumes.load.threads.num=2, dataDirs=2)
18:47:00.141 INFO  Storage - Lock on /tmp/minicluster_storage189662454199067357/data/data1/in_use.lock acquired by nodename 3117@pkrvmf6wy0o8zjz
18:47:00.141 INFO  Storage - Storage directory with location [DISK]file:/tmp/minicluster_storage189662454199067357/data/data1 is not formatted for namespace 734173944. Formatting...
18:47:00.141 INFO  Storage - Generated new storageID DS-e6349f8c-036f-468b-a6a5-1bbd6defa081 for directory /tmp/minicluster_storage189662454199067357/data/data1 
18:47:00.142 INFO  audit - allowed=true	ugi=runner (auth:SIMPLE)	ip=/127.0.0.1	cmd=datanodeReport	src=null	dst=null	perm=null	proto=rpc
18:47:00.142 INFO  MiniDFSCluster - dnInfo.length != numDataNodes
18:47:00.142 INFO  MiniDFSCluster - Waiting for cluster to become active
18:47:00.143 INFO  Storage - Lock on /tmp/minicluster_storage189662454199067357/data/data2/in_use.lock acquired by nodename 3117@pkrvmf6wy0o8zjz
18:47:00.143 INFO  Storage - Storage directory with location [DISK]file:/tmp/minicluster_storage189662454199067357/data/data2 is not formatted for namespace 734173944. Formatting...
18:47:00.143 INFO  Storage - Generated new storageID DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe for directory /tmp/minicluster_storage189662454199067357/data/data2 
18:47:00.156 INFO  Storage - Analyzing storage directories for bpid BP-63767602-10.1.0.176-1747680419830
18:47:00.157 INFO  Storage - Locking is disabled for /tmp/minicluster_storage189662454199067357/data/data1/current/BP-63767602-10.1.0.176-1747680419830
18:47:00.157 INFO  Storage - Block pool storage directory for location [DISK]file:/tmp/minicluster_storage189662454199067357/data/data1 and block pool id BP-63767602-10.1.0.176-1747680419830 is not formatted. Formatting ...
18:47:00.157 INFO  Storage - Formatting block pool BP-63767602-10.1.0.176-1747680419830 directory /tmp/minicluster_storage189662454199067357/data/data1/current/BP-63767602-10.1.0.176-1747680419830/current
18:47:00.170 INFO  Storage - Analyzing storage directories for bpid BP-63767602-10.1.0.176-1747680419830
18:47:00.170 INFO  Storage - Locking is disabled for /tmp/minicluster_storage189662454199067357/data/data2/current/BP-63767602-10.1.0.176-1747680419830
18:47:00.170 INFO  Storage - Block pool storage directory for location [DISK]file:/tmp/minicluster_storage189662454199067357/data/data2 and block pool id BP-63767602-10.1.0.176-1747680419830 is not formatted. Formatting ...
18:47:00.170 INFO  Storage - Formatting block pool BP-63767602-10.1.0.176-1747680419830 directory /tmp/minicluster_storage189662454199067357/data/data2/current/BP-63767602-10.1.0.176-1747680419830/current
18:47:00.171 INFO  DataNode - Setting up storage: nsid=734173944;bpid=BP-63767602-10.1.0.176-1747680419830;lv=-57;nsInfo=lv=-66;cid=testClusterID;nsid=734173944;c=1747680419830;bpid=BP-63767602-10.1.0.176-1747680419830;dnuuid=null
18:47:00.173 INFO  DataNode - Generated and persisted new Datanode UUID e7ab14df-4184-4f87-964c-5990775da0f5
18:47:00.173 INFO  FsDatasetImpl - The datanode lock is a read write lock
18:47:00.174 INFO  FsDatasetImpl - Added new volume: DS-e6349f8c-036f-468b-a6a5-1bbd6defa081
18:47:00.174 INFO  FsDatasetImpl - Added volume - [DISK]file:/tmp/minicluster_storage189662454199067357/data/data1, StorageType: DISK
18:47:00.174 INFO  FsDatasetImpl - Added new volume: DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe
18:47:00.174 INFO  FsDatasetImpl - Added volume - [DISK]file:/tmp/minicluster_storage189662454199067357/data/data2, StorageType: DISK
18:47:00.174 INFO  MemoryMappableBlockLoader - Initializing cache loader: MemoryMappableBlockLoader.
18:47:00.175 INFO  FsDatasetImpl - Registered FSDatasetState MBean
18:47:00.175 INFO  FsDatasetImpl - Adding block pool BP-63767602-10.1.0.176-1747680419830
18:47:00.175 INFO  FsDatasetImpl - Scanning block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data1...
18:47:00.175 INFO  FsDatasetImpl - Scanning block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data2...
18:47:00.175 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage189662454199067357/data/data1/current/BP-63767602-10.1.0.176-1747680419830/current, will proceed with Du for space computation calculation, 
18:47:00.176 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage189662454199067357/data/data2/current/BP-63767602-10.1.0.176-1747680419830/current, will proceed with Du for space computation calculation, 
18:47:00.186 INFO  FsDatasetImpl - Time taken to scan block pool BP-63767602-10.1.0.176-1747680419830 on /tmp/minicluster_storage189662454199067357/data/data1: 11ms
18:47:00.187 INFO  FsDatasetImpl - Time taken to scan block pool BP-63767602-10.1.0.176-1747680419830 on /tmp/minicluster_storage189662454199067357/data/data2: 11ms
18:47:00.187 INFO  FsDatasetImpl - Total time to scan all replicas for block pool BP-63767602-10.1.0.176-1747680419830: 12ms
18:47:00.187 INFO  FsDatasetImpl - Adding replicas to map for block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data1...
18:47:00.187 INFO  BlockPoolSlice - Replica Cache file: /tmp/minicluster_storage189662454199067357/data/data1/current/BP-63767602-10.1.0.176-1747680419830/current/replicas doesn't exist 
18:47:00.187 INFO  FsDatasetImpl - Adding replicas to map for block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data2...
18:47:00.187 INFO  BlockPoolSlice - Replica Cache file: /tmp/minicluster_storage189662454199067357/data/data2/current/BP-63767602-10.1.0.176-1747680419830/current/replicas doesn't exist 
18:47:00.187 INFO  FsDatasetImpl - Time to add replicas to map for block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data1: 1ms
18:47:00.187 INFO  FsDatasetImpl - Time to add replicas to map for block pool BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data2: 1ms
18:47:00.187 INFO  FsDatasetImpl - Total time to add all replicas to map for block pool BP-63767602-10.1.0.176-1747680419830: 1ms
18:47:00.187 INFO  ThrottledAsyncChecker - Scheduling a check for /tmp/minicluster_storage189662454199067357/data/data1
18:47:00.188 INFO  DatasetVolumeChecker - Scheduled health check for volume /tmp/minicluster_storage189662454199067357/data/data1
18:47:00.188 INFO  ThrottledAsyncChecker - Scheduling a check for /tmp/minicluster_storage189662454199067357/data/data2
18:47:00.188 INFO  DatasetVolumeChecker - Scheduled health check for volume /tmp/minicluster_storage189662454199067357/data/data2
18:47:00.188 INFO  VolumeScanner - Now scanning bpid BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data1
18:47:00.188 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
18:47:00.188 INFO  VolumeScanner - Now scanning bpid BP-63767602-10.1.0.176-1747680419830 on volume /tmp/minicluster_storage189662454199067357/data/data2
18:47:00.188 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage189662454199067357/data/data1, DS-e6349f8c-036f-468b-a6a5-1bbd6defa081): finished scanning block pool BP-63767602-10.1.0.176-1747680419830
18:47:00.188 INFO  DirectoryScanner - Periodic Directory Tree Verification scan starting in 158839ms with interval of 21600000ms and throttle limit of -1ms/s
18:47:00.188 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage189662454199067357/data/data2, DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe): finished scanning block pool BP-63767602-10.1.0.176-1747680419830
18:47:00.188 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage189662454199067357/data/data1, DS-e6349f8c-036f-468b-a6a5-1bbd6defa081): no suitable block pools found to scan.  Waiting 1814400000 ms.
18:47:00.188 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage189662454199067357/data/data2, DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe): no suitable block pools found to scan.  Waiting 1814400000 ms.
18:47:00.188 INFO  DataNode - Block pool BP-63767602-10.1.0.176-1747680419830 (Datanode Uuid e7ab14df-4184-4f87-964c-5990775da0f5) service to localhost/127.0.0.1:46347 beginning handshake with NN
18:47:00.189 INFO  StateChange - BLOCK* registerDatanode: from DatanodeRegistration(127.0.0.1:36579, datanodeUuid=e7ab14df-4184-4f87-964c-5990775da0f5, infoPort=33801, infoSecurePort=0, ipcPort=33939, storageInfo=lv=-57;cid=testClusterID;nsid=734173944;c=1747680419830) storage e7ab14df-4184-4f87-964c-5990775da0f5
18:47:00.189 INFO  NetworkTopology - Adding a new node: /default-rack/127.0.0.1:36579
18:47:00.189 INFO  BlockReportLeaseManager - Registered DN e7ab14df-4184-4f87-964c-5990775da0f5 (127.0.0.1:36579).
18:47:00.189 INFO  DataNode - Block pool BP-63767602-10.1.0.176-1747680419830 (Datanode Uuid e7ab14df-4184-4f87-964c-5990775da0f5) service to localhost/127.0.0.1:46347 successfully registered with NN
18:47:00.189 INFO  DataNode - For namenode localhost/127.0.0.1:46347 using BLOCKREPORT_INTERVAL of 21600000msecs CACHEREPORT_INTERVAL of 10000msecs Initial delay: 0msecs; heartBeatInterval=3000
18:47:00.189 INFO  DataNode - Starting IBR Task Handler.
18:47:00.190 INFO  DatanodeDescriptor - Adding new storage ID DS-e6349f8c-036f-468b-a6a5-1bbd6defa081 for DN 127.0.0.1:36579
18:47:00.190 INFO  DatanodeDescriptor - Adding new storage ID DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe for DN 127.0.0.1:36579
18:47:00.190 INFO  DataNode - After receiving heartbeat response, updating state of namenode localhost:46347 to active
18:47:00.190 INFO  BlockStateChange - BLOCK* processReport 0x7d3df4392d6a8ba5 with lease ID 0xef4f322a2e3620e2: Processing first storage report for DS-e6349f8c-036f-468b-a6a5-1bbd6defa081 from datanode DatanodeRegistration(127.0.0.1:36579, datanodeUuid=e7ab14df-4184-4f87-964c-5990775da0f5, infoPort=33801, infoSecurePort=0, ipcPort=33939, storageInfo=lv=-57;cid=testClusterID;nsid=734173944;c=1747680419830)
18:47:00.190 INFO  BlockStateChange - BLOCK* processReport 0x7d3df4392d6a8ba5 with lease ID 0xef4f322a2e3620e2: from storage DS-e6349f8c-036f-468b-a6a5-1bbd6defa081 node DatanodeRegistration(127.0.0.1:36579, datanodeUuid=e7ab14df-4184-4f87-964c-5990775da0f5, infoPort=33801, infoSecurePort=0, ipcPort=33939, storageInfo=lv=-57;cid=testClusterID;nsid=734173944;c=1747680419830), blocks: 0, hasStaleStorage: true, processing time: 0 msecs, invalidatedBlocks: 0
18:47:00.190 INFO  BlockStateChange - BLOCK* processReport 0x7d3df4392d6a8ba5 with lease ID 0xef4f322a2e3620e2: Processing first storage report for DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe from datanode DatanodeRegistration(127.0.0.1:36579, datanodeUuid=e7ab14df-4184-4f87-964c-5990775da0f5, infoPort=33801, infoSecurePort=0, ipcPort=33939, storageInfo=lv=-57;cid=testClusterID;nsid=734173944;c=1747680419830)
18:47:00.190 INFO  BlockStateChange - BLOCK* processReport 0x7d3df4392d6a8ba5 with lease ID 0xef4f322a2e3620e2: from storage DS-fd37c836-57a7-4462-bb9f-cbde227bf7fe node DatanodeRegistration(127.0.0.1:36579, datanodeUuid=e7ab14df-4184-4f87-964c-5990775da0f5, infoPort=33801, infoSecurePort=0, ipcPort=33939, storageInfo=lv=-57;cid=testClusterID;nsid=734173944;c=1747680419830), blocks: 0, hasStaleStorage: false, processing time: 0 msecs, invalidatedBlocks: 0
18:47:00.191 INFO  DataNode - Successfully sent block report 0x7d3df4392d6a8ba5 with lease ID 0xef4f322a2e3620e2 to namenode: localhost/127.0.0.1:46347,  containing 2 storage report(s), of which we sent 2. The reports had 0 total blocks and used 1 RPC(s). This took 0 msecs to generate and 1 msecs for RPC and NN processing. Got back one command: FinalizeCommand/5.
18:47:00.191 INFO  DataNode - Got finalize command for block pool BP-63767602-10.1.0.176-1747680419830
18:47:00.242 INFO  audit - allowed=true	ugi=runner (auth:SIMPLE)	ip=/127.0.0.1	cmd=datanodeReport	src=null	dst=null	perm=null	proto=rpc
18:47:00.242 INFO  MiniDFSCluster - Cluster is active
18:47:00.250 INFO  MemoryStore - Block broadcast_616 stored as values in memory (estimated size 3.0 KiB, free 1920.0 MiB)
18:47:00.251 INFO  MemoryStore - Block broadcast_616_piece0 stored as bytes in memory (estimated size 525.0 B, free 1920.0 MiB)
18:47:00.251 INFO  BlockManagerInfo - Added broadcast_616_piece0 in memory on localhost:45727 (size: 525.0 B, free: 1920.0 MiB)
18:47:00.251 INFO  SparkContext - Created broadcast 616 from broadcast at VcfSink.java:65
18:47:00.254 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
18:47:00.254 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
18:47:00.254 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18:47:00.272 INFO  SparkContext - Starting job: runJob at SparkHadoopWriter.scala:83
18:47:00.272 INFO  DAGScheduler - Registering RDD 1485 (mapToPair at VariantsSparkSink.java:140) as input to shuffle 53
18:47:00.273 INFO  DAGScheduler - Got job 228 (runJob at SparkHadoopWriter.scala:83) with 1 output partitions
18:47:00.273 INFO  DAGScheduler - Final stage: ResultStage 293 (runJob at SparkHadoopWriter.scala:83)
18:47:00.273 INFO  DAGScheduler - Parents of final stage: List(ShuffleMapStage 292)
18:47:00.273 INFO  DAGScheduler - Missing parents: List(ShuffleMapStage 292)
18:47:00.273 INFO  DAGScheduler - Submitting ShuffleMapStage 292 (MapPartitionsRDD[1485] at mapToPair at VariantsSparkSink.java:140), which has no missing parents
18:47:00.274 INFO  MemoryStore - Block broadcast_617 stored as values in memory (estimated size 6.5 KiB, free 1920.0 MiB)
18:47:00.274 INFO  MemoryStore - Block broadcast_617_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1920.0 MiB)
18:47:00.274 INFO  BlockManagerInfo - Added broadcast_617_piece0 in memory on localhost:45727 (size: 3.7 KiB, free: 1920.0 MiB)
18:47:00.275 INFO  SparkContext - Created broadcast 617 from broadcast at DAGScheduler.scala:1580
18:47:00.275 INFO  DAGScheduler - Submitting 4 missing tasks from ShuffleMapStage 292 (MapPartitionsRDD[1485] at mapToPair at VariantsSparkSink.java:140) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
18:47:00.275 INFO  TaskSchedulerImpl - Adding task set 292.0 with 4 tasks resource profile 0
18:47:00.276 INFO  TaskSetManager - Starting task 0.0 in stage 292.0 (TID 379) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8087 bytes) 
18:47:00.276 INFO  TaskSetManager - Starting task 1.0 in stage 292.0 (TID 380) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8193 bytes) 
18:47:00.276 INFO  TaskSetManager - Starting task 2.0 in stage 292.0 (TID 381) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8087 bytes) 
18:47:00.277 INFO  TaskSetManager - Starting task 3.0 in stage 292.0 (TID 382) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8193 bytes) 
18:47:00.277 INFO  Executor - Running task 0.0 in stage 292.0 (TID 379)
18:47:00.277 INFO  Executor - Running task 1.0 in stage 292.0 (TID 380)
18:47:00.277 INFO  Executor - Running task 3.0 in stage 292.0 (TID 382)
18:47:00.277 INFO  Executor - Running task 2.0 in stage 292.0 (TID 381)
18:47:00.289 INFO  Executor - Finished task 2.0 in stage 292.0 (TID 381). 1062 bytes result sent to driver
18:47:00.289 INFO  Executor - Finished task 3.0 in stage 292.0 (TID 382). 1062 bytes result sent to driver
18:47:00.289 INFO  Executor - Finished task 1.0 in stage 292.0 (TID 380). 1062 bytes result sent to driver
18:47:00.290 INFO  TaskSetManager - Finished task 2.0 in stage 292.0 (TID 381) in 14 ms on localhost (executor driver) (1/4)
18:47:00.290 INFO  TaskSetManager - Finished task 3.0 in stage 292.0 (TID 382) in 14 ms on localhost (executor driver) (2/4)
18:47:00.290 INFO  TaskSetManager - Finished task 1.0 in stage 292.0 (TID 380) in 14 ms on localhost (executor driver) (3/4)
18:47:00.291 INFO  Executor - Finished task 0.0 in stage 292.0 (TID 379). 1062 bytes result sent to driver
18:47:00.292 INFO  TaskSetManager - Finished task 0.0 in stage 292.0 (TID 379) in 17 ms on localhost (executor driver) (4/4)
18:47:00.292 INFO  TaskSchedulerImpl - Removed TaskSet 292.0, whose tasks have all completed, from pool 
18:47:00.292 INFO  DAGScheduler - ShuffleMapStage 292 (mapToPair at VariantsSparkSink.java:140) finished in 0.019 s
18:47:00.292 INFO  DAGScheduler - looking for newly runnable stages
18:47:00.292 INFO  DAGScheduler - running: HashSet()
18:47:00.292 INFO  DAGScheduler - waiting: HashSet(ResultStage 293)
18:47:00.292 INFO  DAGScheduler - failed: HashSet()
18:47:00.292 INFO  DAGScheduler - Submitting ResultStage 293 (MapPartitionsRDD[1489] at mapToPair at VcfSink.java:77), which has no missing parents
18:47:00.298 INFO  MemoryStore - Block broadcast_618 stored as values in memory (estimated size 149.6 KiB, free 1919.8 MiB)
18:47:00.299 INFO  MemoryStore - Block broadcast_618_piece0 stored as bytes in memory (estimated size 56.1 KiB, free 1919.8 MiB)
18:47:00.299 INFO  BlockManagerInfo - Added broadcast_618_piece0 in memory on localhost:45727 (size: 56.1 KiB, free: 1919.9 MiB)
18:47:00.299 INFO  SparkContext - Created broadcast 618 from broadcast at DAGScheduler.scala:1580
18:47:00.299 INFO  DAGScheduler - Submitting 1 missing tasks from ResultStage 293 (MapPartitionsRDD[1489] at mapToPair at VcfSink.java:77) (first 15 tasks are for partitions Vector(0))
18:47:00.299 INFO  TaskSchedulerImpl - Adding task set 293.0 with 1 tasks resource profile 0
18:47:00.300 INFO  TaskSetManager - Starting task 0.0 in stage 293.0 (TID 383) (localhost, executor driver, partition 0, NODE_LOCAL, 7513 bytes) 
18:47:00.300 INFO  Executor - Running task 0.0 in stage 293.0 (TID 383)
18:47:00.308 INFO  ShuffleBlockFetcherIterator - Getting 4 (1336.0 B) non-empty blocks including 4 (1336.0 B) local and 0 (0.0 B) host-local and 0 (0.0 B) push-merged-local and 0 (0.0 B) remote blocks
18:47:00.308 INFO  ShuffleBlockFetcherIterator - Started 0 remote fetches in 0 ms
18:47:00.315 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
18:47:00.315 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
18:47:00.315 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18:47:00.315 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
18:47:00.315 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
18:47:00.315 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18:47:00.329 INFO  FileOutputCommitter - Saved output of task 'attempt_202505191847001496014474308038793_1489_r_000000_0' to file:/tmp/VariantsSparkSinkUnitTest4220594662402443626.vcf.parts/_temporary/0/task_202505191847001496014474308038793_1489_r_000000
18:47:00.329 INFO  SparkHadoopMapRedUtil - attempt_202505191847001496014474308038793_1489_r_000000_0: Committed. Elapsed time: 0 ms.
18:47:00.329 INFO  Executor - Finished task 0.0 in stage 293.0 (TID 383). 1858 bytes result sent to driver
18:47:00.330 INFO  TaskSetManager - Finished task 0.0 in stage 293.0 (TID 383) in 30 ms on localhost (executor driver) (1/1)
18:47:00.330 INFO  TaskSchedulerImpl - Removed TaskSet 293.0, whose tasks have all completed, from pool 
18:47:00.330 INFO  DAGScheduler - ResultStage 293 (runJob at SparkHadoopWriter.scala:83) finished in 0.038 s
18:47:00.330 INFO  DAGScheduler - Job 228 is finished. Cancelling potential speculative or zombie tasks for this job
18:47:00.330 INFO  TaskSchedulerImpl - Killing all running tasks in stage 293: Stage finished
18:47:00.330 INFO  DAGScheduler - Job 228 finished: runJob at SparkHadoopWriter.scala:83, took 0.058227 s
18:47:00.330 INFO  SparkHadoopWriter - Start to commit write Job job_202505191847001496014474308038793_1489.
18:47:00.336 INFO  SparkHadoopWriter - Write Job job_202505191847001496014474308038793_1489 committed. Elapsed time: 5 ms.
18:47:00.344 INFO  HadoopFileSystemWrapper - Concatenating 2 parts to /tmp/VariantsSparkSinkUnitTest4220594662402443626.vcf
18:47:00.348 INFO  HadoopFileSystemWrapper - Concatenating to /tmp/VariantsSparkSinkUnitTest4220594662402443626.vcf done
[May 19, 2025 at 6:47:00 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 6:47:00 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 6:47:00 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[May 19, 2025 at 6:47:00 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600