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

32

tests

0

failures

0

ignored

19.910s

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) 0.173s passed
testEnableDisableGVCFWriting[1](false, .vcf.gz) 0.158s passed
testEnableDisableGVCFWriting[2](true, .g.vcf) 0.164s passed
testEnableDisableGVCFWriting[3](true, .g.vcf.gz) 0.161s passed
testWritingToAnExistingFileHDFS[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 1.175s passed
testWritingToAnExistingFileHDFS[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 1.528s passed
testWritingToAnExistingFileHDFS[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.672s passed
testWritingToAnExistingFileHDFS[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 2.352s passed
testWritingToAnExistingFileHDFS[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 1.090s passed
testWritingToAnExistingFileHDFS[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 1.081s passed
testWritingToFileURL[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 0.218s passed
testWritingToFileURL[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 0.255s passed
testWritingToFileURL[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.215s passed
testWritingToFileURL[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 0.248s passed
testWritingToFileURL[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 0.234s passed
testWritingToFileURL[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 0.222s passed
variantsSinkHDFSTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 1.057s passed
variantsSinkHDFSTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 2.292s passed
variantsSinkHDFSTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.676s passed
variantsSinkHDFSTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 2.256s passed
variantsSinkHDFSTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 1.439s passed
variantsSinkHDFSTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 1.013s passed
variantsSinkTest[0](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf, true) 0.185s passed
variantsSinkTest[1](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, true) 0.212s passed
variantsSinkTest[2](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.bgz, false) 0.218s passed
variantsSinkTest[3](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, true) 0.199s passed
variantsSinkTest[4](/home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf, .vcf.gz, false) 0.196s passed
variantsSinkTest[5](/home/runner/work/gatk/gatk/src/test/resources/HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf, .vcf, true) 0.220s passed

Standard error

17:38:30.513 INFO  MiniDFSCluster - starting cluster: numNameNodes=1, numDataNodes=1
17:38:30.514 INFO  NameNode - Formatting using clusterid: testClusterID
17:38:30.514 INFO  FSEditLog - Edit logging is async:true
17:38:30.522 INFO  FSNamesystem - KeyProvider: null
17:38:30.522 INFO  FSNamesystem - fsLock is fair: true
17:38:30.522 INFO  FSNamesystem - Detailed lock hold time metrics enabled: false
17:38:30.522 INFO  FSNamesystem - fsOwner                = runner (auth:SIMPLE)
17:38:30.522 INFO  FSNamesystem - supergroup             = supergroup
17:38:30.522 INFO  FSNamesystem - isPermissionEnabled    = true
17:38:30.522 INFO  FSNamesystem - isStoragePolicyEnabled = true
17:38:30.522 INFO  FSNamesystem - HA Enabled: false
17:38:30.522 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
17:38:30.522 INFO  DatanodeManager - dfs.block.invalidate.limit : configured=1000, counted=60, effected=1000
17:38:30.522 INFO  DatanodeManager - dfs.namenode.datanode.registration.ip-hostname-check=true
17:38:30.522 INFO  BlockManager - dfs.namenode.startup.delay.block.deletion.sec is set to 000:00:00:00.000
17:38:30.522 INFO  BlockManager - The block deletion will start around 2025 Oct 27 17:38:30
17:38:30.522 INFO  GSet - Computing capacity for map BlocksMap
17:38:30.522 INFO  GSet - VM type       = 64-bit
17:38:30.522 INFO  GSet - 2.0% max memory 3.4 GB = 70 MB
17:38:30.522 INFO  GSet - capacity      = 2^23 = 8388608 entries
17:38:30.523 INFO  BlockManager - Storage policy satisfier is disabled
17:38:30.523 INFO  BlockManager - dfs.block.access.token.enable = false
17:38:30.523 INFO  BlockManagerSafeMode - dfs.namenode.safemode.threshold-pct = 0.999
17:38:30.523 INFO  BlockManagerSafeMode - dfs.namenode.safemode.min.datanodes = 0
17:38:30.523 INFO  BlockManagerSafeMode - dfs.namenode.safemode.extension = 0
17:38:30.523 INFO  BlockManager - defaultReplication         = 1
17:38:30.523 INFO  BlockManager - maxReplication             = 512
17:38:30.523 INFO  BlockManager - minReplication             = 1
17:38:30.523 INFO  BlockManager - maxReplicationStreams      = 2
17:38:30.523 INFO  BlockManager - redundancyRecheckInterval  = 3000ms
17:38:30.523 INFO  BlockManager - encryptDataTransfer        = false
17:38:30.523 INFO  BlockManager - maxNumBlocksToLog          = 1000
17:38:30.523 INFO  GSet - Computing capacity for map INodeMap
17:38:30.523 INFO  GSet - VM type       = 64-bit
17:38:30.523 INFO  GSet - 1.0% max memory 3.4 GB = 35 MB
17:38:30.523 INFO  GSet - capacity      = 2^22 = 4194304 entries
17:38:30.524 INFO  FSDirectory - ACLs enabled? true
17:38:30.524 INFO  FSDirectory - POSIX ACL inheritance enabled? true
17:38:30.524 INFO  FSDirectory - XAttrs enabled? true
17:38:30.524 INFO  NameNode - Caching file names occurring more than 10 times
17:38:30.524 INFO  SnapshotManager - Loaded config captureOpenFiles: false, skipCaptureAccessTimeOnlyChange: false, snapshotDiffAllowSnapRootDescendant: true, maxSnapshotLimit: 65536
17:38:30.524 INFO  SnapshotManager - SkipList is disabled
17:38:30.524 INFO  GSet - Computing capacity for map cachedBlocks
17:38:30.524 INFO  GSet - VM type       = 64-bit
17:38:30.524 INFO  GSet - 0.25% max memory 3.4 GB = 8.8 MB
17:38:30.524 INFO  GSet - capacity      = 2^20 = 1048576 entries
17:38:30.524 INFO  TopMetrics - NNTop conf: dfs.namenode.top.window.num.buckets = 10
17:38:30.524 INFO  TopMetrics - NNTop conf: dfs.namenode.top.num.users = 10
17:38:30.524 INFO  TopMetrics - NNTop conf: dfs.namenode.top.windows.minutes = 1,5,25
17:38:30.524 INFO  FSNamesystem - Retry cache on namenode is enabled
17:38:30.524 INFO  FSNamesystem - Retry cache will use 0.03 of total heap and retry cache entry expiry time is 600000 millis
17:38:30.524 INFO  GSet - Computing capacity for map NameNodeRetryCache
17:38:30.524 INFO  GSet - VM type       = 64-bit
17:38:30.524 INFO  GSet - 0.029999999329447746% max memory 3.4 GB = 1.0 MB
17:38:30.524 INFO  GSet - capacity      = 2^17 = 131072 entries
17:38:30.525 INFO  FSImage - Allocated new BlockPoolId: BP-1020663005-10.1.0.252-1761586710524
17:38:30.534 INFO  Storage - Storage directory /tmp/minicluster_storage11963465818520545253/name-0-1 has been successfully formatted.
17:38:30.542 INFO  Storage - Storage directory /tmp/minicluster_storage11963465818520545253/name-0-2 has been successfully formatted.
17:38:30.550 INFO  FSImageFormatProtobuf - Saving image file /tmp/minicluster_storage11963465818520545253/name-0-1/current/fsimage.ckpt_0000000000000000000 using no compression
17:38:30.550 INFO  FSImageFormatProtobuf - Saving image file /tmp/minicluster_storage11963465818520545253/name-0-2/current/fsimage.ckpt_0000000000000000000 using no compression
17:38:30.553 INFO  FSImageFormatProtobuf - Image file /tmp/minicluster_storage11963465818520545253/name-0-2/current/fsimage.ckpt_0000000000000000000 of size 419 bytes saved in 0 seconds .
17:38:30.553 INFO  FSImageFormatProtobuf - Image file /tmp/minicluster_storage11963465818520545253/name-0-1/current/fsimage.ckpt_0000000000000000000 of size 419 bytes saved in 0 seconds .
17:38:30.561 INFO  NNStorageRetentionManager - Going to retain 1 images with txid >= 0
17:38:30.572 INFO  FSNamesystem - Stopping services started for active state
17:38:30.572 INFO  FSNamesystem - Stopping services started for standby state
17:38:30.572 INFO  BlockManagerInfo - Removed broadcast_615_piece0 on localhost:37953 in memory (size: 154.0 KiB, free: 1920.0 MiB)
17:38:30.572 INFO  NameNode - createNameNode []
17:38:30.573 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
17:38:30.574 INFO  BlockManagerInfo - Removed broadcast_614_piece0 on localhost:37953 in memory (size: 50.2 KiB, free: 1920.0 MiB)
17:38:30.574 INFO  MetricsSystemImpl - Scheduled Metric snapshot period at 10 second(s).
17:38:30.574 INFO  MetricsSystemImpl - NameNode metrics system started
17:38:30.575 INFO  NameNodeUtils - fs.defaultFS is hdfs://127.0.0.1:0
17:38:30.584 INFO  JvmPauseMonitor - Starting JVM pause monitor
17:38:30.584 INFO  DFSUtil - Filter initializers set : org.apache.hadoop.http.lib.StaticUserWebFilter,org.apache.hadoop.hdfs.web.AuthFilterInitializer
17:38:30.584 INFO  DFSUtil - Starting Web-server for hdfs at: http://localhost:0
17:38:30.585 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
17:38:30.585 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:38:30.586 INFO  HttpServer2 - Added global filter 'safety' (class=org.apache.hadoop.http.HttpServer2$QuotingInputFilter)
17:38:30.586 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context hdfs
17:38:30.586 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context static
17:38:30.587 INFO  HttpServer2 - Added filter AuthFilter (class=org.apache.hadoop.hdfs.web.AuthFilter) to context hdfs
17:38:30.587 INFO  HttpServer2 - Added filter AuthFilter (class=org.apache.hadoop.hdfs.web.AuthFilter) to context static
17:38:30.587 INFO  HttpServer2 - addJerseyResourcePackage: packageName=org.apache.hadoop.hdfs.server.namenode.web.resources;org.apache.hadoop.hdfs.web.resources, pathSpec=/webhdfs/v1/*
17:38:30.587 INFO  HttpServer2 - Jetty bound to port 35081
17:38:30.587 INFO  Server - jetty-9.4.56.v20240826; built: 2024-08-26T17:15:05.868Z; git: ec6782ff5ead824dabdcf47fa98f90a4aedff401; jvm 17.0.6+10
17:38:30.588 INFO  session - DefaultSessionIdManager workerName=node0
17:38:30.588 INFO  session - No SessionScavenger set, using defaults
17:38:30.588 INFO  session - node0 Scavenging every 660000ms
17:38:30.589 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
17:38:30.589 INFO  ContextHandler - Started o.e.j.s.ServletContextHandler@79e5d3c1{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}
17:38:30.658 INFO  ContextHandler - Started o.e.j.w.WebAppContext@387d8334{hdfs,/,file:///tmp/jetty-localhost-35081-hadoop-hdfs-3_3_6-tests_jar-_-any-6031043120155364825/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}
17:38:30.659 INFO  AbstractConnector - Started ServerConnector@63c4e26a{HTTP/1.1, (http/1.1)}{localhost:35081}
17:38:30.659 INFO  Server - Started @72771ms
17:38:30.659 INFO  FSEditLog - Edit logging is async:true
17:38:30.668 INFO  FSNamesystem - KeyProvider: null
17:38:30.668 INFO  FSNamesystem - fsLock is fair: true
17:38:30.668 INFO  FSNamesystem - Detailed lock hold time metrics enabled: false
17:38:30.668 INFO  FSNamesystem - fsOwner                = runner (auth:SIMPLE)
17:38:30.668 INFO  FSNamesystem - supergroup             = supergroup
17:38:30.668 INFO  FSNamesystem - isPermissionEnabled    = true
17:38:30.668 INFO  FSNamesystem - isStoragePolicyEnabled = true
17:38:30.668 INFO  FSNamesystem - HA Enabled: false
17:38:30.668 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
17:38:30.668 INFO  DatanodeManager - dfs.block.invalidate.limit : configured=1000, counted=60, effected=1000
17:38:30.668 INFO  DatanodeManager - dfs.namenode.datanode.registration.ip-hostname-check=true
17:38:30.668 INFO  BlockManager - dfs.namenode.startup.delay.block.deletion.sec is set to 000:00:00:00.000
17:38:30.668 INFO  BlockManager - The block deletion will start around 2025 Oct 27 17:38:30
17:38:30.668 INFO  GSet - Computing capacity for map BlocksMap
17:38:30.668 INFO  GSet - VM type       = 64-bit
17:38:30.668 INFO  GSet - 2.0% max memory 3.4 GB = 70 MB
17:38:30.668 INFO  GSet - capacity      = 2^23 = 8388608 entries
17:38:30.669 INFO  BlockManager - Storage policy satisfier is disabled
17:38:30.669 INFO  BlockManager - dfs.block.access.token.enable = false
17:38:30.669 INFO  BlockManagerSafeMode - dfs.namenode.safemode.threshold-pct = 0.999
17:38:30.669 INFO  BlockManagerSafeMode - dfs.namenode.safemode.min.datanodes = 0
17:38:30.669 INFO  BlockManagerSafeMode - dfs.namenode.safemode.extension = 0
17:38:30.669 INFO  BlockManager - defaultReplication         = 1
17:38:30.669 INFO  BlockManager - maxReplication             = 512
17:38:30.669 INFO  BlockManager - minReplication             = 1
17:38:30.669 INFO  BlockManager - maxReplicationStreams      = 2
17:38:30.669 INFO  BlockManager - redundancyRecheckInterval  = 3000ms
17:38:30.669 INFO  BlockManager - encryptDataTransfer        = false
17:38:30.669 INFO  BlockManager - maxNumBlocksToLog          = 1000
17:38:30.669 INFO  GSet - Computing capacity for map INodeMap
17:38:30.669 INFO  GSet - VM type       = 64-bit
17:38:30.669 INFO  GSet - 1.0% max memory 3.4 GB = 35 MB
17:38:30.669 INFO  GSet - capacity      = 2^22 = 4194304 entries
17:38:30.670 INFO  FSDirectory - ACLs enabled? true
17:38:30.670 INFO  FSDirectory - POSIX ACL inheritance enabled? true
17:38:30.670 INFO  FSDirectory - XAttrs enabled? true
17:38:30.670 INFO  NameNode - Caching file names occurring more than 10 times
17:38:30.670 INFO  SnapshotManager - Loaded config captureOpenFiles: false, skipCaptureAccessTimeOnlyChange: false, snapshotDiffAllowSnapRootDescendant: true, maxSnapshotLimit: 65536
17:38:30.670 INFO  SnapshotManager - SkipList is disabled
17:38:30.670 INFO  GSet - Computing capacity for map cachedBlocks
17:38:30.670 INFO  GSet - VM type       = 64-bit
17:38:30.670 INFO  GSet - 0.25% max memory 3.4 GB = 8.8 MB
17:38:30.670 INFO  GSet - capacity      = 2^20 = 1048576 entries
17:38:30.670 INFO  TopMetrics - NNTop conf: dfs.namenode.top.window.num.buckets = 10
17:38:30.670 INFO  TopMetrics - NNTop conf: dfs.namenode.top.num.users = 10
17:38:30.670 INFO  TopMetrics - NNTop conf: dfs.namenode.top.windows.minutes = 1,5,25
17:38:30.670 INFO  FSNamesystem - Retry cache on namenode is enabled
17:38:30.670 INFO  FSNamesystem - Retry cache will use 0.03 of total heap and retry cache entry expiry time is 600000 millis
17:38:30.670 INFO  GSet - Computing capacity for map NameNodeRetryCache
17:38:30.670 INFO  GSet - VM type       = 64-bit
17:38:30.670 INFO  GSet - 0.029999999329447746% max memory 3.4 GB = 1.0 MB
17:38:30.670 INFO  GSet - capacity      = 2^17 = 131072 entries
17:38:30.675 INFO  Storage - Lock on /tmp/minicluster_storage11963465818520545253/name-0-1/in_use.lock acquired by nodename 2975@runnervmrcw8b
17:38:30.678 INFO  Storage - Lock on /tmp/minicluster_storage11963465818520545253/name-0-2/in_use.lock acquired by nodename 2975@runnervmrcw8b
17:38:30.679 INFO  FileJournalManager - Recovering unfinalized segments in /tmp/minicluster_storage11963465818520545253/name-0-1/current
17:38:30.679 INFO  FileJournalManager - Recovering unfinalized segments in /tmp/minicluster_storage11963465818520545253/name-0-2/current
17:38:30.679 INFO  FSImage - No edit log streams selected.
17:38:30.679 INFO  FSImage - Planning to load image: FSImageFile(file=/tmp/minicluster_storage11963465818520545253/name-0-1/current/fsimage_0000000000000000000, cpktTxId=0000000000000000000)
17:38:30.680 INFO  FSImageFormatPBINode - Loading 1 INodes.
17:38:30.680 INFO  FSImageFormatPBINode - Successfully loaded 1 inodes
17:38:30.680 INFO  FSImageFormatPBINode - Completed update blocks map and name cache, total waiting duration 0ms.
17:38:30.680 INFO  FSImageFormatProtobuf - Loaded FSImage in 0 seconds.
17:38:30.680 INFO  FSImage - Loaded image for txid 0 from /tmp/minicluster_storage11963465818520545253/name-0-1/current/fsimage_0000000000000000000
17:38:30.680 INFO  FSNamesystem - Need to save fs image? false (staleImage=false, haEnabled=false, isRollingUpgrade=false)
17:38:30.680 INFO  FSEditLog - Starting log segment at 1
17:38:30.689 INFO  NameCache - initialized with 0 entries 0 lookups
17:38:30.689 INFO  FSNamesystem - Finished loading FSImage in 18 msecs
17:38:30.689 INFO  NameNode - RPC server is binding to localhost:0
17:38:30.689 INFO  NameNode - Enable NameNode state context:false
17:38:30.689 INFO  CallQueueManager - Using callQueue: class java.util.concurrent.LinkedBlockingQueue, queueCapacity: 1000, scheduler: class org.apache.hadoop.ipc.DefaultRpcScheduler, ipcBackoff: false.
17:38:30.689 INFO  Server - Listener at localhost:33453
17:38:30.689 INFO  Server - Starting Socket Reader #1 for port 0
17:38:30.691 INFO  NameNode - Clients are to use localhost:33453 to access this namenode/service.
17:38:30.691 INFO  FSNamesystem - Registered FSNamesystemState, ReplicatedBlocksState and ECBlockGroupsState MBeans.
17:38:30.699 INFO  LeaseManager - Number of blocks under construction: 0
17:38:30.699 INFO  DatanodeAdminDefaultMonitor - Initialized the Default Decommission and Maintenance monitor
17:38:30.700 INFO  BlockManager - Start MarkedDeleteBlockScrubber thread
17:38:30.700 INFO  BlockManager - initializing replication queues
17:38:30.700 INFO  StateChange - STATE* Leaving safe mode after 0 secs
17:38:30.700 INFO  StateChange - STATE* Network topology has 0 racks and 0 datanodes
17:38:30.700 INFO  StateChange - STATE* UnderReplicatedBlocks has 0 blocks
17:38:30.702 INFO  Server - IPC Server Responder: starting
17:38:30.703 INFO  Server - IPC Server listener on 0: starting
17:38:30.703 INFO  BlockManager - Total number of blocks            = 0
17:38:30.703 INFO  BlockManager - Number of invalid blocks          = 0
17:38:30.703 INFO  BlockManager - Number of under-replicated blocks = 0
17:38:30.703 INFO  BlockManager - Number of  over-replicated blocks = 0
17:38:30.703 INFO  BlockManager - Number of blocks being written    = 0
17:38:30.703 INFO  StateChange - STATE* Replication Queue initialization scan for invalid, over- and under-replicated blocks completed in 3 msec
17:38:30.704 INFO  NameNode - NameNode RPC up at: localhost/127.0.0.1:33453
17:38:30.704 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:38:30.704 INFO  FSNamesystem - Starting services required for active state
17:38:30.704 INFO  FSDirectory - Initializing quota with 12 thread(s)
17:38:30.705 INFO  FSDirectory - Quota initialization completed in 1 milliseconds
name space=1
storage space=0
storage types=RAM_DISK=0, SSD=0, DISK=0, ARCHIVE=0, PROVIDED=0
17:38:30.705 INFO  CacheReplicationMonitor - Starting CacheReplicationMonitor with interval 30000 milliseconds
17:38:30.706 INFO  MiniDFSCluster - Starting DataNode 0 with dfs.datanode.data.dir: [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data1,[DISK]file:/tmp/minicluster_storage11963465818520545253/data/data2
17:38:30.706 INFO  ThrottledAsyncChecker - Scheduling a check for [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data1
17:38:30.707 INFO  ThrottledAsyncChecker - Scheduling a check for [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data2
17:38:30.712 INFO  MetricsSystemImpl - DataNode metrics system started (again)
17:38:30.712 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
17:38:30.712 INFO  BlockScanner - Initialized block scanner with targetBytesPerSec 1048576
17:38:30.713 INFO  DataNode - Configured hostname is 127.0.0.1
17:38:30.713 INFO  Util - dfs.datanode.fileio.profiling.sampling.percentage set to 0. Disabling file IO profiling
17:38:30.713 INFO  DataNode - Starting DataNode with maxLockedMemory = 0
17:38:30.713 INFO  DataNode - Opened streaming server at /127.0.0.1:43375
17:38:30.713 INFO  DataNode - Balancing bandwidth is 104857600 bytes/s
17:38:30.713 INFO  DataNode - Number threads for balancing is 100
17:38:30.715 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
17:38:30.715 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:38:30.716 INFO  HttpServer2 - Added global filter 'safety' (class=org.apache.hadoop.http.HttpServer2$QuotingInputFilter)
17:38:30.716 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context datanode
17:38:30.716 INFO  HttpServer2 - Added filter static_user_filter (class=org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter) to context static
17:38:30.717 INFO  HttpServer2 - Jetty bound to port 40149
17:38:30.717 INFO  Server - jetty-9.4.56.v20240826; built: 2024-08-26T17:15:05.868Z; git: ec6782ff5ead824dabdcf47fa98f90a4aedff401; jvm 17.0.6+10
17:38:30.717 INFO  session - DefaultSessionIdManager workerName=node0
17:38:30.717 INFO  session - No SessionScavenger set, using defaults
17:38:30.718 INFO  session - node0 Scavenging every 600000ms
17:38:30.718 INFO  ContextHandler - Started o.e.j.s.ServletContextHandler@f258afc{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}
17:38:30.787 INFO  ContextHandler - Started o.e.j.w.WebAppContext@4f31c3a0{datanode,/,file:///tmp/jetty-localhost-40149-hadoop-hdfs-3_3_6-tests_jar-_-any-15474884245583497095/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}
17:38:30.787 INFO  AbstractConnector - Started ServerConnector@53e59233{HTTP/1.1, (http/1.1)}{localhost:40149}
17:38:30.787 INFO  Server - Started @72899ms
17:38:30.788 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
17:38:30.789 INFO  DatanodeHttpServer - Listening HTTP traffic on /127.0.0.1:39991
17:38:30.789 INFO  DataNode - dnUserName = runner
17:38:30.789 INFO  DataNode - supergroup = supergroup
17:38:30.789 INFO  JvmPauseMonitor - Starting JVM pause monitor
17:38:30.790 INFO  CallQueueManager - Using callQueue: class java.util.concurrent.LinkedBlockingQueue, queueCapacity: 1000, scheduler: class org.apache.hadoop.ipc.DefaultRpcScheduler, ipcBackoff: false.
17:38:30.790 INFO  Server - Listener at localhost:33413
17:38:30.790 INFO  Server - Starting Socket Reader #1 for port 0
17:38:30.792 INFO  DataNode - Opened IPC server at /127.0.0.1:33413
17:38:30.801 INFO  DataNode - Refresh request received for nameservices: null
17:38:30.801 INFO  DataNode - Starting BPOfferServices for nameservices: <default>
17:38:30.801 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:38:30.801 INFO  DataNode - Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:33453 starting to offer service
17:38:30.802 INFO  Server - IPC Server Responder: starting
17:38:30.802 INFO  Server - IPC Server listener on 0: starting
17:38:30.803 INFO  DataNode - Acknowledging ACTIVE Namenode during handshakeBlock pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:33453
17:38:30.803 INFO  Storage - Using 2 threads to upgrade data directories (dfs.datanode.parallel.volumes.load.threads.num=2, dataDirs=2)
17:38:30.805 INFO  audit - allowed=true	ugi=runner (auth:SIMPLE)	ip=/127.0.0.1	cmd=datanodeReport	src=null	dst=null	perm=null	proto=rpc
17:38:30.806 INFO  MiniDFSCluster - dnInfo.length != numDataNodes
17:38:30.806 INFO  MiniDFSCluster - Waiting for cluster to become active
17:38:30.810 INFO  Storage - Lock on /tmp/minicluster_storage11963465818520545253/data/data1/in_use.lock acquired by nodename 2975@runnervmrcw8b
17:38:30.810 INFO  Storage - Storage directory with location [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data1 is not formatted for namespace 1363701927. Formatting...
17:38:30.810 INFO  Storage - Generated new storageID DS-73c72c6c-97b2-4d32-a416-75947812aa3a for directory /tmp/minicluster_storage11963465818520545253/data/data1 
17:38:30.820 INFO  Storage - Lock on /tmp/minicluster_storage11963465818520545253/data/data2/in_use.lock acquired by nodename 2975@runnervmrcw8b
17:38:30.821 INFO  Storage - Storage directory with location [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data2 is not formatted for namespace 1363701927. Formatting...
17:38:30.821 INFO  Storage - Generated new storageID DS-ace7fd1b-a958-4531-963c-7b5c144c70a3 for directory /tmp/minicluster_storage11963465818520545253/data/data2 
17:38:30.838 INFO  Storage - Analyzing storage directories for bpid BP-1020663005-10.1.0.252-1761586710524
17:38:30.838 INFO  Storage - Locking is disabled for /tmp/minicluster_storage11963465818520545253/data/data1/current/BP-1020663005-10.1.0.252-1761586710524
17:38:30.838 INFO  Storage - Block pool storage directory for location [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data1 and block pool id BP-1020663005-10.1.0.252-1761586710524 is not formatted. Formatting ...
17:38:30.838 INFO  Storage - Formatting block pool BP-1020663005-10.1.0.252-1761586710524 directory /tmp/minicluster_storage11963465818520545253/data/data1/current/BP-1020663005-10.1.0.252-1761586710524/current
17:38:30.854 INFO  Storage - Analyzing storage directories for bpid BP-1020663005-10.1.0.252-1761586710524
17:38:30.854 INFO  Storage - Locking is disabled for /tmp/minicluster_storage11963465818520545253/data/data2/current/BP-1020663005-10.1.0.252-1761586710524
17:38:30.854 INFO  Storage - Block pool storage directory for location [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data2 and block pool id BP-1020663005-10.1.0.252-1761586710524 is not formatted. Formatting ...
17:38:30.854 INFO  Storage - Formatting block pool BP-1020663005-10.1.0.252-1761586710524 directory /tmp/minicluster_storage11963465818520545253/data/data2/current/BP-1020663005-10.1.0.252-1761586710524/current
17:38:30.862 INFO  DataNode - Setting up storage: nsid=1363701927;bpid=BP-1020663005-10.1.0.252-1761586710524;lv=-57;nsInfo=lv=-66;cid=testClusterID;nsid=1363701927;c=1761586710524;bpid=BP-1020663005-10.1.0.252-1761586710524;dnuuid=null
17:38:30.871 INFO  DataNode - Generated and persisted new Datanode UUID 4bb6331f-167f-4ad3-abdf-baed64f0590a
17:38:30.871 INFO  FsDatasetImpl - The datanode lock is a read write lock
17:38:30.872 INFO  FsDatasetImpl - Added new volume: DS-73c72c6c-97b2-4d32-a416-75947812aa3a
17:38:30.872 INFO  FsDatasetImpl - Added volume - [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data1, StorageType: DISK
17:38:30.873 INFO  FsDatasetImpl - Added new volume: DS-ace7fd1b-a958-4531-963c-7b5c144c70a3
17:38:30.873 INFO  FsDatasetImpl - Added volume - [DISK]file:/tmp/minicluster_storage11963465818520545253/data/data2, StorageType: DISK
17:38:30.873 INFO  MemoryMappableBlockLoader - Initializing cache loader: MemoryMappableBlockLoader.
17:38:30.873 INFO  FsDatasetImpl - Registered FSDatasetState MBean
17:38:30.874 INFO  FsDatasetImpl - Adding block pool BP-1020663005-10.1.0.252-1761586710524
17:38:30.874 INFO  FsDatasetImpl - Scanning block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data1...
17:38:30.874 INFO  FsDatasetImpl - Scanning block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data2...
17:38:30.874 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage11963465818520545253/data/data1/current/BP-1020663005-10.1.0.252-1761586710524/current, will proceed with Du for space computation calculation, 
17:38:30.874 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage11963465818520545253/data/data2/current/BP-1020663005-10.1.0.252-1761586710524/current, will proceed with Du for space computation calculation, 
17:38:30.885 INFO  FsDatasetImpl - Time taken to scan block pool BP-1020663005-10.1.0.252-1761586710524 on /tmp/minicluster_storage11963465818520545253/data/data2: 11ms
17:38:30.885 INFO  FsDatasetImpl - Time taken to scan block pool BP-1020663005-10.1.0.252-1761586710524 on /tmp/minicluster_storage11963465818520545253/data/data1: 11ms
17:38:30.885 INFO  FsDatasetImpl - Total time to scan all replicas for block pool BP-1020663005-10.1.0.252-1761586710524: 11ms
17:38:30.886 INFO  FsDatasetImpl - Adding replicas to map for block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data1...
17:38:30.886 INFO  BlockPoolSlice - Replica Cache file: /tmp/minicluster_storage11963465818520545253/data/data1/current/BP-1020663005-10.1.0.252-1761586710524/current/replicas doesn't exist 
17:38:30.886 INFO  FsDatasetImpl - Adding replicas to map for block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data2...
17:38:30.886 INFO  BlockPoolSlice - Replica Cache file: /tmp/minicluster_storage11963465818520545253/data/data2/current/BP-1020663005-10.1.0.252-1761586710524/current/replicas doesn't exist 
17:38:30.886 INFO  FsDatasetImpl - Time to add replicas to map for block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data1: 0ms
17:38:30.886 INFO  FsDatasetImpl - Time to add replicas to map for block pool BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data2: 0ms
17:38:30.886 INFO  FsDatasetImpl - Total time to add all replicas to map for block pool BP-1020663005-10.1.0.252-1761586710524: 1ms
17:38:30.886 INFO  ThrottledAsyncChecker - Scheduling a check for /tmp/minicluster_storage11963465818520545253/data/data1
17:38:30.886 INFO  DatasetVolumeChecker - Scheduled health check for volume /tmp/minicluster_storage11963465818520545253/data/data1
17:38:30.887 INFO  ThrottledAsyncChecker - Scheduling a check for /tmp/minicluster_storage11963465818520545253/data/data2
17:38:30.887 INFO  DatasetVolumeChecker - Scheduled health check for volume /tmp/minicluster_storage11963465818520545253/data/data2
17:38:30.887 INFO  VolumeScanner - Now scanning bpid BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data1
17:38:30.887 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
17:38:30.887 INFO  VolumeScanner - Now scanning bpid BP-1020663005-10.1.0.252-1761586710524 on volume /tmp/minicluster_storage11963465818520545253/data/data2
17:38:30.887 INFO  DirectoryScanner - Periodic Directory Tree Verification scan starting in 19589253ms with interval of 21600000ms and throttle limit of -1ms/s
17:38:30.887 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage11963465818520545253/data/data2, DS-ace7fd1b-a958-4531-963c-7b5c144c70a3): finished scanning block pool BP-1020663005-10.1.0.252-1761586710524
17:38:30.887 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage11963465818520545253/data/data1, DS-73c72c6c-97b2-4d32-a416-75947812aa3a): finished scanning block pool BP-1020663005-10.1.0.252-1761586710524
17:38:30.887 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage11963465818520545253/data/data2, DS-ace7fd1b-a958-4531-963c-7b5c144c70a3): no suitable block pools found to scan.  Waiting 1814400000 ms.
17:38:30.887 INFO  VolumeScanner - VolumeScanner(/tmp/minicluster_storage11963465818520545253/data/data1, DS-73c72c6c-97b2-4d32-a416-75947812aa3a): no suitable block pools found to scan.  Waiting 1814400000 ms.
17:38:30.887 INFO  DataNode - Block pool BP-1020663005-10.1.0.252-1761586710524 (Datanode Uuid 4bb6331f-167f-4ad3-abdf-baed64f0590a) service to localhost/127.0.0.1:33453 beginning handshake with NN
17:38:30.888 INFO  StateChange - BLOCK* registerDatanode: from DatanodeRegistration(127.0.0.1:43375, datanodeUuid=4bb6331f-167f-4ad3-abdf-baed64f0590a, infoPort=39991, infoSecurePort=0, ipcPort=33413, storageInfo=lv=-57;cid=testClusterID;nsid=1363701927;c=1761586710524) storage 4bb6331f-167f-4ad3-abdf-baed64f0590a
17:38:30.888 INFO  NetworkTopology - Adding a new node: /default-rack/127.0.0.1:43375
17:38:30.888 INFO  BlockReportLeaseManager - Registered DN 4bb6331f-167f-4ad3-abdf-baed64f0590a (127.0.0.1:43375).
17:38:30.888 INFO  DataNode - Block pool BP-1020663005-10.1.0.252-1761586710524 (Datanode Uuid 4bb6331f-167f-4ad3-abdf-baed64f0590a) service to localhost/127.0.0.1:33453 successfully registered with NN
17:38:30.889 INFO  DataNode - For namenode localhost/127.0.0.1:33453 using BLOCKREPORT_INTERVAL of 21600000msecs CACHEREPORT_INTERVAL of 10000msecs Initial delay: 0msecs; heartBeatInterval=3000
17:38:30.889 INFO  DataNode - Starting IBR Task Handler.
17:38:30.889 INFO  DatanodeDescriptor - Adding new storage ID DS-73c72c6c-97b2-4d32-a416-75947812aa3a for DN 127.0.0.1:43375
17:38:30.889 INFO  DatanodeDescriptor - Adding new storage ID DS-ace7fd1b-a958-4531-963c-7b5c144c70a3 for DN 127.0.0.1:43375
17:38:30.889 INFO  DataNode - After receiving heartbeat response, updating state of namenode localhost:33453 to active
17:38:30.890 INFO  BlockStateChange - BLOCK* processReport 0x5ee5db274e1ad75d with lease ID 0x95224fd454a3d867: Processing first storage report for DS-ace7fd1b-a958-4531-963c-7b5c144c70a3 from datanode DatanodeRegistration(127.0.0.1:43375, datanodeUuid=4bb6331f-167f-4ad3-abdf-baed64f0590a, infoPort=39991, infoSecurePort=0, ipcPort=33413, storageInfo=lv=-57;cid=testClusterID;nsid=1363701927;c=1761586710524)
17:38:30.890 INFO  BlockStateChange - BLOCK* processReport 0x5ee5db274e1ad75d with lease ID 0x95224fd454a3d867: from storage DS-ace7fd1b-a958-4531-963c-7b5c144c70a3 node DatanodeRegistration(127.0.0.1:43375, datanodeUuid=4bb6331f-167f-4ad3-abdf-baed64f0590a, infoPort=39991, infoSecurePort=0, ipcPort=33413, storageInfo=lv=-57;cid=testClusterID;nsid=1363701927;c=1761586710524), blocks: 0, hasStaleStorage: true, processing time: 0 msecs, invalidatedBlocks: 0
17:38:30.890 INFO  BlockStateChange - BLOCK* processReport 0x5ee5db274e1ad75d with lease ID 0x95224fd454a3d867: Processing first storage report for DS-73c72c6c-97b2-4d32-a416-75947812aa3a from datanode DatanodeRegistration(127.0.0.1:43375, datanodeUuid=4bb6331f-167f-4ad3-abdf-baed64f0590a, infoPort=39991, infoSecurePort=0, ipcPort=33413, storageInfo=lv=-57;cid=testClusterID;nsid=1363701927;c=1761586710524)
17:38:30.890 INFO  BlockStateChange - BLOCK* processReport 0x5ee5db274e1ad75d with lease ID 0x95224fd454a3d867: from storage DS-73c72c6c-97b2-4d32-a416-75947812aa3a node DatanodeRegistration(127.0.0.1:43375, datanodeUuid=4bb6331f-167f-4ad3-abdf-baed64f0590a, infoPort=39991, infoSecurePort=0, ipcPort=33413, storageInfo=lv=-57;cid=testClusterID;nsid=1363701927;c=1761586710524), blocks: 0, hasStaleStorage: false, processing time: 0 msecs, invalidatedBlocks: 0
17:38:30.890 INFO  DataNode - Successfully sent block report 0x5ee5db274e1ad75d with lease ID 0x95224fd454a3d867 to namenode: localhost/127.0.0.1:33453,  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.
17:38:30.890 INFO  DataNode - Got finalize command for block pool BP-1020663005-10.1.0.252-1761586710524
17:38:30.906 INFO  audit - allowed=true	ugi=runner (auth:SIMPLE)	ip=/127.0.0.1	cmd=datanodeReport	src=null	dst=null	perm=null	proto=rpc
17:38:30.906 INFO  MiniDFSCluster - Cluster is active
17:38:30.915 INFO  MemoryStore - Block broadcast_616 stored as values in memory (estimated size 3.0 KiB, free 1920.0 MiB)
17:38:30.916 INFO  MemoryStore - Block broadcast_616_piece0 stored as bytes in memory (estimated size 525.0 B, free 1920.0 MiB)
17:38:30.916 INFO  BlockManagerInfo - Added broadcast_616_piece0 in memory on localhost:37953 (size: 525.0 B, free: 1920.0 MiB)
17:38:30.916 INFO  SparkContext - Created broadcast 616 from broadcast at VcfSink.java:65
17:38:30.920 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
17:38:30.920 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
17:38:30.920 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
17:38:30.933 INFO  SparkContext - Starting job: runJob at SparkHadoopWriter.scala:83
17:38:30.934 INFO  DAGScheduler - Registering RDD 1485 (mapToPair at VariantsSparkSink.java:140) as input to shuffle 53
17:38:30.934 INFO  DAGScheduler - Got job 228 (runJob at SparkHadoopWriter.scala:83) with 1 output partitions
17:38:30.934 INFO  DAGScheduler - Final stage: ResultStage 293 (runJob at SparkHadoopWriter.scala:83)
17:38:30.934 INFO  DAGScheduler - Parents of final stage: List(ShuffleMapStage 292)
17:38:30.934 INFO  DAGScheduler - Missing parents: List(ShuffleMapStage 292)
17:38:30.934 INFO  DAGScheduler - Submitting ShuffleMapStage 292 (MapPartitionsRDD[1485] at mapToPair at VariantsSparkSink.java:140), which has no missing parents
17:38:30.936 INFO  MemoryStore - Block broadcast_617 stored as values in memory (estimated size 6.5 KiB, free 1920.0 MiB)
17:38:30.936 INFO  MemoryStore - Block broadcast_617_piece0 stored as bytes in memory (estimated size 3.7 KiB, free 1920.0 MiB)
17:38:30.936 INFO  BlockManagerInfo - Added broadcast_617_piece0 in memory on localhost:37953 (size: 3.7 KiB, free: 1920.0 MiB)
17:38:30.937 INFO  SparkContext - Created broadcast 617 from broadcast at DAGScheduler.scala:1580
17:38:30.937 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))
17:38:30.937 INFO  TaskSchedulerImpl - Adding task set 292.0 with 4 tasks resource profile 0
17:38:30.938 INFO  TaskSetManager - Starting task 0.0 in stage 292.0 (TID 379) (localhost, executor driver, partition 0, PROCESS_LOCAL, 8087 bytes) 
17:38:30.938 INFO  TaskSetManager - Starting task 1.0 in stage 292.0 (TID 380) (localhost, executor driver, partition 1, PROCESS_LOCAL, 8193 bytes) 
17:38:30.939 INFO  TaskSetManager - Starting task 2.0 in stage 292.0 (TID 381) (localhost, executor driver, partition 2, PROCESS_LOCAL, 8087 bytes) 
17:38:30.939 INFO  TaskSetManager - Starting task 3.0 in stage 292.0 (TID 382) (localhost, executor driver, partition 3, PROCESS_LOCAL, 8193 bytes) 
17:38:30.939 INFO  Executor - Running task 0.0 in stage 292.0 (TID 379)
17:38:30.940 INFO  Executor - Running task 1.0 in stage 292.0 (TID 380)
17:38:30.940 INFO  Executor - Running task 2.0 in stage 292.0 (TID 381)
17:38:30.940 INFO  Executor - Running task 3.0 in stage 292.0 (TID 382)
17:38:30.951 INFO  Executor - Finished task 3.0 in stage 292.0 (TID 382). 1062 bytes result sent to driver
17:38:30.952 INFO  TaskSetManager - Finished task 3.0 in stage 292.0 (TID 382) in 13 ms on localhost (executor driver) (1/4)
17:38:30.953 INFO  Executor - Finished task 1.0 in stage 292.0 (TID 380). 1062 bytes result sent to driver
17:38:30.955 INFO  TaskSetManager - Finished task 1.0 in stage 292.0 (TID 380) in 17 ms on localhost (executor driver) (2/4)
17:38:30.955 INFO  Executor - Finished task 2.0 in stage 292.0 (TID 381). 1062 bytes result sent to driver
17:38:30.956 INFO  Executor - Finished task 0.0 in stage 292.0 (TID 379). 1062 bytes result sent to driver
17:38:30.956 INFO  TaskSetManager - Finished task 2.0 in stage 292.0 (TID 381) in 17 ms on localhost (executor driver) (3/4)
17:38:30.956 INFO  TaskSetManager - Finished task 0.0 in stage 292.0 (TID 379) in 19 ms on localhost (executor driver) (4/4)
17:38:30.956 INFO  TaskSchedulerImpl - Removed TaskSet 292.0, whose tasks have all completed, from pool 
17:38:30.956 INFO  DAGScheduler - ShuffleMapStage 292 (mapToPair at VariantsSparkSink.java:140) finished in 0.021 s
17:38:30.956 INFO  DAGScheduler - looking for newly runnable stages
17:38:30.956 INFO  DAGScheduler - running: HashSet()
17:38:30.956 INFO  DAGScheduler - waiting: HashSet(ResultStage 293)
17:38:30.956 INFO  DAGScheduler - failed: HashSet()
17:38:30.956 INFO  DAGScheduler - Submitting ResultStage 293 (MapPartitionsRDD[1489] at mapToPair at VcfSink.java:77), which has no missing parents
17:38:30.962 INFO  MemoryStore - Block broadcast_618 stored as values in memory (estimated size 149.6 KiB, free 1919.8 MiB)
17:38:30.963 INFO  MemoryStore - Block broadcast_618_piece0 stored as bytes in memory (estimated size 56.2 KiB, free 1919.8 MiB)
17:38:30.963 INFO  BlockManagerInfo - Added broadcast_618_piece0 in memory on localhost:37953 (size: 56.2 KiB, free: 1919.9 MiB)
17:38:30.963 INFO  SparkContext - Created broadcast 618 from broadcast at DAGScheduler.scala:1580
17:38:30.963 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))
17:38:30.963 INFO  TaskSchedulerImpl - Adding task set 293.0 with 1 tasks resource profile 0
17:38:30.964 INFO  TaskSetManager - Starting task 0.0 in stage 293.0 (TID 383) (localhost, executor driver, partition 0, NODE_LOCAL, 7513 bytes) 
17:38:30.965 INFO  Executor - Running task 0.0 in stage 293.0 (TID 383)
17:38:30.971 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
17:38:30.971 INFO  ShuffleBlockFetcherIterator - Started 0 remote fetches in 0 ms
17:38:30.978 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
17:38:30.978 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
17:38:30.978 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
17:38:30.978 INFO  PathOutputCommitterFactory - No output committer factory defined, defaulting to FileOutputCommitterFactory
17:38:30.978 INFO  FileOutputCommitter - File Output Committer Algorithm version is 1
17:38:30.978 INFO  FileOutputCommitter - FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
17:38:30.987 INFO  FileOutputCommitter - Saved output of task 'attempt_202510271738302895750774353596007_1489_r_000000_0' to file:/tmp/VariantsSparkSinkUnitTest17816793289542943728.vcf.parts/_temporary/0/task_202510271738302895750774353596007_1489_r_000000
17:38:30.987 INFO  SparkHadoopMapRedUtil - attempt_202510271738302895750774353596007_1489_r_000000_0: Committed. Elapsed time: 0 ms.
17:38:30.988 INFO  Executor - Finished task 0.0 in stage 293.0 (TID 383). 1858 bytes result sent to driver
17:38:30.988 INFO  TaskSetManager - Finished task 0.0 in stage 293.0 (TID 383) in 24 ms on localhost (executor driver) (1/1)
17:38:30.988 INFO  TaskSchedulerImpl - Removed TaskSet 293.0, whose tasks have all completed, from pool 
17:38:30.989 INFO  DAGScheduler - ResultStage 293 (runJob at SparkHadoopWriter.scala:83) finished in 0.032 s
17:38:30.989 INFO  DAGScheduler - Job 228 is finished. Cancelling potential speculative or zombie tasks for this job
17:38:30.989 INFO  TaskSchedulerImpl - Killing all running tasks in stage 293: Stage finished
17:38:30.989 INFO  DAGScheduler - Job 228 finished: runJob at SparkHadoopWriter.scala:83, took 0.055216 s
17:38:30.989 INFO  SparkHadoopWriter - Start to commit write Job job_202510271738302895750774353596007_1489.
17:38:30.992 INFO  SparkHadoopWriter - Write Job job_202510271738302895750774353596007_1489 committed. Elapsed time: 3 ms.
17:38:30.998 INFO  HadoopFileSystemWrapper - Concatenating 2 parts to /tmp/VariantsSparkSinkUnitTest17816793289542943728.vcf
17:38:31.001 INFO  HadoopFileSystemWrapper - Concatenating to /tmp/VariantsSparkSinkUnitTest17816793289542943728.vcf done
[October 27, 2025 at 5:38:31 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[October 27, 2025 at 5:38:31 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[October 27, 2025 at 5:38:31 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600
[October 27, 2025 at 5:38:31 PM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=629145600