2019-10-07 18:10:07 Hail: WARN: This Hail JAR was compiled for Spark 2.4.0, running with Spark 2.4.4. Compatibility is not guaranteed. 2019-10-07 18:10:07 SparkContext: INFO: Running Spark version 2.4.4 2019-10-07 18:10:07 SparkContext: INFO: Submitted application: Hail 2019-10-07 18:10:07 SparkContext: INFO: Spark configuration: spark.app.name=Hail spark.driver.extraClassPath=/opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar spark.driver.extraJavaOptions=-Xss4M spark.driver.maxResultSize=0 spark.driver.memory=41g spark.dynamicAllocation.enabled=true spark.dynamicAllocation.maxExecutors=10000 spark.dynamicAllocation.minExecutors=1 spark.eventLog.dir=hdfs://mw-m/user/spark/eventlog spark.eventLog.enabled=true spark.executor.cores=4 spark.executor.extraClassPath=./hail-all-spark.jar spark.executor.extraJavaOptions=-Xss4M spark.executor.instances=2 spark.executor.memory=18619m spark.executorEnv.OPENBLAS_NUM_THREADS=1 spark.executorEnv.PYTHONHASHSEED=0 spark.hadoop.hive.execution.engine=mr spark.hadoop.io.compression.codecs=org.apache.hadoop.io.compress.DefaultCodec,is.hail.io.compress.BGzipCodec,is.hail.io.compress.BGzipCodecTbi,org.apache.hadoop.io.compress.GzipCodec spark.hadoop.mapreduce.input.fileinputformat.split.minsize=0 spark.history.fs.logDirectory=hdfs://mw-m/user/spark/eventlog spark.jars=file:/opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator spark.kryoserializer.buffer.max=1g spark.logConf=true spark.master=yarn spark.repl.local.jars=file:///opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar spark.rpc.message.maxSize=512 spark.scheduler.minRegisteredResourcesRatio=0.0 spark.scheduler.mode=FAIR spark.serializer=org.apache.spark.serializer.KryoSerializer spark.shuffle.service.enabled=true spark.sql.cbo.enabled=true spark.sql.parquet.cacheMetadata=false spark.stage.maxConsecutiveAttempts=10 spark.submit.deployMode=client spark.submit.pyFiles=/tmp/005a1c57cb654370bf73cf301202bb67/pyscripts__cb__s3z.zip spark.task.maxFailures=20 spark.ui.showConsoleProgress=false spark.yarn.am.attemptFailuresValidityInterval=1h spark.yarn.am.memory=640m spark.yarn.dist.jars=file:///opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar spark.yarn.dist.pyFiles=file:///tmp/005a1c57cb654370bf73cf301202bb67/pyscripts__cb__s3z.zip spark.yarn.executor.failuresValidityInterval=1h spark.yarn.historyServer.address=mw-m:18080 spark.yarn.isPython=true spark.yarn.jars=local:/usr/lib/spark/jars/* spark.yarn.tags=dataproc_hash_e4394056-b411-392b-9490-f3f2184ae816,dataproc_job_005a1c57cb654370bf73cf301202bb67,dataproc_master_index_0,dataproc_uuid_b683544f-9ab7-3354-9c24-af5151532d07 2019-10-07 18:10:08 SecurityManager: INFO: Changing view acls to: root 2019-10-07 18:10:08 SecurityManager: INFO: Changing modify acls to: root 2019-10-07 18:10:08 SecurityManager: INFO: Changing view acls groups to: 2019-10-07 18:10:08 SecurityManager: INFO: Changing modify acls groups to: 2019-10-07 18:10:08 SecurityManager: INFO: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(root); groups with view permissions: Set(); users with modify permissions: Set(root); groups with modify permissions: Set() 2019-10-07 18:10:08 Utils: INFO: Successfully started service 'sparkDriver' on port 34209. 2019-10-07 18:10:08 SparkEnv: INFO: Registering MapOutputTracker 2019-10-07 18:10:08 SparkEnv: INFO: Registering BlockManagerMaster 2019-10-07 18:10:08 BlockManagerMasterEndpoint: INFO: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information 2019-10-07 18:10:08 BlockManagerMasterEndpoint: INFO: BlockManagerMasterEndpoint up 2019-10-07 18:10:08 DiskBlockManager: INFO: Created local directory at /hadoop/spark/tmp/blockmgr-768a9d2c-a08f-4380-804e-ed52558d9355 2019-10-07 18:10:08 MemoryStore: INFO: MemoryStore started with capacity 21.7 GB 2019-10-07 18:10:08 SparkEnv: INFO: Registering OutputCommitCoordinator 2019-10-07 18:10:08 log: INFO: Logging initialized @4263ms 2019-10-07 18:10:08 Server: INFO: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown 2019-10-07 18:10:08 Server: INFO: Started @4351ms 2019-10-07 18:10:08 Utils: WARN: Service 'SparkUI' could not bind on port 4040. Attempting port 4041. 2019-10-07 18:10:08 AbstractConnector: INFO: Started ServerConnector@ee7ac84{HTTP/1.1,[http/1.1]}{0.0.0.0:4041} 2019-10-07 18:10:08 Utils: INFO: Successfully started service 'SparkUI' on port 4041. 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@32329736{/jobs,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@631c6995{/jobs/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@682722f4{/jobs/job,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@76f3cafc{/jobs/job/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@27926654{/stages,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@31a76029{/stages/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@5dc35bc4{/stages/stage,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@bb730ab{/stages/stage/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@4ced4762{/stages/pool,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@75c2adb{/stages/pool/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@5bef23df{/storage,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@69ef7261{/storage/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@4f9ffe69{/storage/rdd,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@29f31fb3{/storage/rdd/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@b202089{/environment,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@194e37f6{/environment/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@2912fe00{/executors,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@182d6216{/executors/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@12833df2{/executors/threadDump,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@7a9a49d3{/executors/threadDump/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@44464a7e{/static,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@5f425afd{/,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@320205bd{/api,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@58568ddc{/jobs/job/kill,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@63b6e503{/stages/stage/kill,null,AVAILABLE,@Spark} 2019-10-07 18:10:08 SparkUI: INFO: Bound SparkUI to 0.0.0.0, and started at http://mw-m.c.broad-mpg-gnomad.internal:4041 2019-10-07 18:10:08 SparkContext: INFO: Added JAR file:/opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar at spark://mw-m.c.broad-mpg-gnomad.internal:34209/jars/hail-all-spark.jar with timestamp 1570471808661 2019-10-07 18:10:08 FairSchedulableBuilder: WARN: Fair Scheduler configuration file not found so jobs will be scheduled in FIFO order. To use fair scheduling, configure pools in fairscheduler.xml or set spark.scheduler.allocation.file to a file that contains the configuration. 2019-10-07 18:10:08 FairSchedulableBuilder: INFO: Created default pool: default, schedulingMode: FIFO, minShare: 0, weight: 1 2019-10-07 18:10:08 Utils: INFO: Using initial executors = 2, max of spark.dynamicAllocation.initialExecutors, spark.dynamicAllocation.minExecutors and spark.executor.instances 2019-10-07 18:10:09 RMProxy: INFO: Connecting to ResourceManager at mw-m/10.128.0.8:8032 2019-10-07 18:10:09 AHSProxy: INFO: Connecting to Application History server at mw-m/10.128.0.8:10200 2019-10-07 18:10:09 Client: INFO: Requesting a new application from cluster with 2 NodeManagers 2019-10-07 18:10:09 Client: INFO: Verifying our application has not requested more than the maximum memory capability of the cluster (40960 MB per container) 2019-10-07 18:10:09 Client: INFO: Will allocate AM container, with 1024 MB memory including 384 MB overhead 2019-10-07 18:10:09 Client: INFO: Setting up container launch context for our AM 2019-10-07 18:10:09 Client: INFO: Setting up the launch environment for our AM container 2019-10-07 18:10:09 Client: INFO: Preparing resources for our AM container 2019-10-07 18:10:09 Client: INFO: Uploading resource file:/opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar -> hdfs://mw-m/user/root/.sparkStaging/application_1570469351427_0002/hail-all-spark.jar 2019-10-07 18:10:09 Client: INFO: Uploading resource file:/usr/lib/spark/python/lib/pyspark.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570469351427_0002/pyspark.zip 2019-10-07 18:10:09 Client: INFO: Uploading resource file:/usr/lib/spark/python/lib/py4j-0.10.7-src.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570469351427_0002/py4j-0.10.7-src.zip 2019-10-07 18:10:09 Client: INFO: Uploading resource file:/tmp/005a1c57cb654370bf73cf301202bb67/pyscripts__cb__s3z.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570469351427_0002/pyscripts__cb__s3z.zip 2019-10-07 18:10:10 Client: INFO: Uploading resource file:/hadoop/spark/tmp/spark-115a38c9-ae53-401a-9f19-b51ab63a1e36/__spark_conf__8015925343901433468.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570469351427_0002/__spark_conf__.zip 2019-10-07 18:10:10 SecurityManager: INFO: Changing view acls to: root 2019-10-07 18:10:10 SecurityManager: INFO: Changing modify acls to: root 2019-10-07 18:10:10 SecurityManager: INFO: Changing view acls groups to: 2019-10-07 18:10:10 SecurityManager: INFO: Changing modify acls groups to: 2019-10-07 18:10:10 SecurityManager: INFO: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(root); groups with view permissions: Set(); users with modify permissions: Set(root); groups with modify permissions: Set() 2019-10-07 18:10:11 Client: INFO: Submitting application application_1570469351427_0002 to ResourceManager 2019-10-07 18:10:11 YarnClientImpl: INFO: Submitted application application_1570469351427_0002 2019-10-07 18:10:11 SchedulerExtensionServices: INFO: Starting Yarn extension services with app application_1570469351427_0002 and attemptId None 2019-10-07 18:10:12 Client: INFO: Application report for application_1570469351427_0002 (state: ACCEPTED) 2019-10-07 18:10:12 Client: INFO: client token: N/A diagnostics: AM container is launched, waiting for AM container to Register with RM ApplicationMaster host: N/A ApplicationMaster RPC port: -1 queue: default start time: 1570471811952 final status: UNDEFINED tracking URL: http://mw-m:8088/proxy/application_1570469351427_0002/ user: root 2019-10-07 18:10:13 Client: INFO: Application report for application_1570469351427_0002 (state: ACCEPTED) 2019-10-07 18:10:14 Client: INFO: Application report for application_1570469351427_0002 (state: ACCEPTED) 2019-10-07 18:10:15 YarnClientSchedulerBackend: INFO: Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> mw-m, PROXY_URI_BASES -> http://mw-m:8088/proxy/application_1570469351427_0002), /proxy/application_1570469351427_0002 2019-10-07 18:10:15 JettyUtils: INFO: Adding filter org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter to /jobs, /jobs/json, /jobs/job, /jobs/job/json, /stages, /stages/json, /stages/stage, /stages/stage/json, /stages/pool, /stages/pool/json, /storage, /storage/json, /storage/rdd, /storage/rdd/json, /environment, /environment/json, /executors, /executors/json, /executors/threadDump, /executors/threadDump/json, /static, /, /api, /jobs/job/kill, /stages/stage/kill. 2019-10-07 18:10:15 YarnSchedulerBackend$YarnSchedulerEndpoint: INFO: ApplicationMaster registered as NettyRpcEndpointRef(spark-client://YarnAM) 2019-10-07 18:10:15 Client: INFO: Application report for application_1570469351427_0002 (state: RUNNING) 2019-10-07 18:10:16 Client: INFO: client token: N/A diagnostics: N/A ApplicationMaster host: 10.128.0.5 ApplicationMaster RPC port: -1 queue: default start time: 1570471811952 final status: UNDEFINED tracking URL: http://mw-m:8088/proxy/application_1570469351427_0002/ user: root 2019-10-07 18:10:16 YarnClientSchedulerBackend: INFO: Application application_1570469351427_0002 has started running. 2019-10-07 18:10:16 Utils: INFO: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 34837. 2019-10-07 18:10:16 NettyBlockTransferService: INFO: Server created on mw-m.c.broad-mpg-gnomad.internal:34837 2019-10-07 18:10:16 BlockManager: INFO: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy 2019-10-07 18:10:16 BlockManagerMaster: INFO: Registering BlockManager BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 34837, None) 2019-10-07 18:10:16 BlockManagerMasterEndpoint: INFO: Registering block manager mw-m.c.broad-mpg-gnomad.internal:34837 with 21.7 GB RAM, BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 34837, None) 2019-10-07 18:10:16 BlockManagerMaster: INFO: Registered BlockManager BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 34837, None) 2019-10-07 18:10:16 BlockManager: INFO: external shuffle service port = 7337 2019-10-07 18:10:16 BlockManager: INFO: Initialized BlockManager: BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 34837, None) 2019-10-07 18:10:16 JettyUtils: INFO: Adding filter org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter to /metrics/json. 2019-10-07 18:10:16 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@61c9b98f{/metrics/json,null,AVAILABLE,@Spark} 2019-10-07 18:10:16 EventLoggingListener: INFO: Logging events to hdfs://mw-m/user/spark/eventlog/application_1570469351427_0002 2019-10-07 18:10:16 Utils: INFO: Using initial executors = 2, max of spark.dynamicAllocation.initialExecutors, spark.dynamicAllocation.minExecutors and spark.executor.instances 2019-10-07 18:10:16 YarnClientSchedulerBackend: INFO: SchedulerBackend is ready for scheduling beginning after reached minRegisteredResourcesRatio: 0.0 2019-10-07 18:10:16 Hail: INFO: Hail temporary directory: hdfs://mw-m/tmp/hail.7cj7uP922FPD 2019-10-07 18:10:16 Hail: INFO: SparkUI: http://mw-m.c.broad-mpg-gnomad.internal:4041 2019-10-07 18:10:16 Hail: INFO: Running Hail version 0.2.24-9cd88d97bedd 2019-10-07 18:10:16 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect. 2019-10-07 18:10:18 ZlibFactory: INFO: Successfully loaded & initialized native-zlib library 2019-10-07 18:10:18 CodecPool: INFO: Got brand-new decompressor [.gz] 2019-10-07 18:10:19 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.5:54000) with ID 1 2019-10-07 18:10:19 ExecutorAllocationManager: INFO: New executor 1 has registered (new total is 1) 2019-10-07 18:10:19 BlockManagerMasterEndpoint: INFO: Registering block manager mw-w-0.c.broad-mpg-gnomad.internal:37157 with 9.5 GB RAM, BlockManagerId(1, mw-w-0.c.broad-mpg-gnomad.internal, 37157, None) 2019-10-07 18:10:19 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 47.4 KB, free 21.7 GB) 2019-10-07 18:10:19 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 2.9 KB, free 21.7 GB) 2019-10-07 18:10:19 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 2.9 KB, free: 21.7 GB) 2019-10-07 18:10:19 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:20 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.10:46280) with ID 2 2019-10-07 18:10:20 ExecutorAllocationManager: INFO: New executor 2 has registered (new total is 2) 2019-10-07 18:10:20 BlockManagerMasterEndpoint: INFO: Registering block manager mw-w-1.c.broad-mpg-gnomad.internal:39849 with 9.5 GB RAM, BlockManagerId(2, mw-w-1.c.broad-mpg-gnomad.internal, 39849, None) 2019-10-07 18:10:22 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 401.3 KB, free 21.7 GB) 2019-10-07 18:10:22 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 28.2 KB, free 21.7 GB) 2019-10-07 18:10:22 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:10:22 SparkContext: INFO: Created broadcast 1 from textFile at RichSparkContext.scala:16 2019-10-07 18:10:22 FileInputFormat: INFO: Total input files to process : 1 2019-10-07 18:10:22 Hail: INFO: Reading table with no type imputation Loading column 'f0' as type 'str' (type not specified) Loading column 'f1' as type 'str' (type not specified) Loading column 'f2' as type 'str' (type not specified) Loading column 'f3' as type 'int32' (user-specified) Loading column 'f4' as type 'int32' (user-specified) Loading column 'f5' as type 'float64' (user-specified) Loading column 'f6' as type 'str' (type not specified) Loading column 'f7' as type 'int32' (user-specified) Loading column 'f8' as type 'str' (type not specified) 2019-10-07 18:10:22 root: INFO: RegionPool: initialized for thread 19: Thread-6 2019-10-07 18:10:22 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 36: (TableAggregate (TableMapRows (TableRename ("f7" "f6" "f1" "f8" "f0" "f5" "f3" "f4" "f2") ("frame" "strand" "source" "attribute" "seqname" "score" "start" "end" "feature") () () (TableRead None False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (InsertFields (SelectFields (seqname source feature start end score strand frame attribute) (Ref row)) None (attribute (ApplyIR dict Dict[String,String] (ArrayMap __uid_7 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ApplyIR indexArray String (Apply split Array[String] (Ref __uid_7) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ApplyIR indexArray String (Apply split Array[String] (Ref __uid_7) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))))) (AggExplode __uid_8 False (ApplyIR keys Array[String] (GetField attribute (Ref row))) (ApplyAggOp CollectAsSet () None ( (Ref __uid_8))))) 2019-10-07 18:10:23 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 33: (TableAggregate (TableRename ("f8") ("attribute") () () (TableRead Table{global:Struct{},key:[],row:Struct{f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (AggExplode __iruid_25 False (ArrayMap __iruid_26 (ToArray (ToDict (ArrayMap __iruid_27 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_27) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_27) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))) (GetField key (Ref __iruid_26))) (ApplyAggOp CollectAsSet () None ( (Ref __iruid_25))))) 2019-10-07 18:10:23 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 33: (TableAggregate (TableRename ("f8") ("attribute") () () (TableRead Table{global:Struct{},key:[],row:Struct{f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (AggExplode __iruid_25 False (ArrayMap __iruid_26 (ToArray (ToDict (ArrayMap __iruid_27 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_27) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_27) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))) (GetField key (Ref __iruid_26))) (ApplyAggOp CollectAsSet () None ( (Ref __iruid_25))))) 2019-10-07 18:10:23 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 33: (TableAggregate (TableRename ("f8") ("attribute") () () (TableRead Table{global:Struct{},key:[],row:Struct{f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (AggExplode __iruid_34 False (ArrayMap __iruid_35 (ToArray (ToDict (ArrayMap __iruid_36 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_36) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_36) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))) (GetField key (Ref __iruid_35))) (ApplyAggOp CollectAsSet () None ( (Ref __iruid_34))))) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 401.3 KB, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 28.2 KB, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 2 from textFile at RichSparkContext.scala:16 2019-10-07 18:10:23 FileInputFormat: INFO: Total input files to process : 1 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_0. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_0.apply instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_0.apply instruction count: 11 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_0.ENCODE_o_tuple_of_END_TO_o_struct_of_END_1 instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeDecode_1. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.apply instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.apply instruction count: 12 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.DECODE_o_struct_of_END_TO_o_tuple_of_END_1 instruction count: 14 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 2.7 KB, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 1014.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 1014.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 3 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 2: (Begin (InitOp2 0 (CollectAsSet () (String) None) ())) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 2: (Begin (InitOp2 0 (CollectAsSet () (String) None) ())) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 4 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.apply instruction count: 52 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.apply instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.newAggState instruction count: 35 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.setAggState instruction count: 71 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.getAggOffset instruction count: 54 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C2.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 32: (Begin (ArrayFor __iruid_34 (ArrayMap __iruid_35 (ToArray (ToDict (ArrayMap __iruid_36 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_36) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_36) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))) (GetField key (Ref __iruid_35))) (Begin (SeqOp2 0 (CollectAsSet () (String) None) ( (Ref __iruid_34)))))) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 32: (Begin (ArrayFor __iruid_46 (ArrayMap __iruid_47 (ToArray (ToDict (ArrayMap __iruid_48 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_48) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_48) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))) (GetField key (Ref __iruid_47))) (Begin (SeqOp2 0 (CollectAsSet () (String) None) ( (Ref __iruid_46)))))) 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4.apply instruction count: 11 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4.apply instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4.method_1 instruction count: 114 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4.method_2 instruction count: 45 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C4.method_3 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_5. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_5.apply instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_5.apply instruction count: 11 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_5.ENCODE_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_stringEND_TO_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryEND_1 instruction count: 97 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C_etypeEncode_5.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 96.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 75.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 75.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.apply instruction count: 22 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.apply instruction count: 20 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.newAggState instruction count: 35 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.setAggState instruction count: 71 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.getAggOffset instruction count: 54 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_11 instruction count: 1114 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_12 instruction count: 103 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_13 instruction count: 106 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_14 instruction count: 329 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_15 instruction count: 150 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_16 instruction count: 33 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.method_17 instruction count: 150 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.DECODE_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryEND_TO_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_stringEND_20 instruction count: 146 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.INPLACE_DECODE_o_binary_TO_o_binary_21 instruction count: 29 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C3.addLiterals instruction count: 58 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 1: (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 1: (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_6 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_6_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 6 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.apply instruction count: 74 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.apply instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.newAggState instruction count: 35 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.setAggState instruction count: 71 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.getAggOffset instruction count: 54 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.DECODE_o_binary_TO_o_string_11 instruction count: 26 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.bulkLoad_12 instruction count: 381 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C6.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 1: (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 1: (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_7 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_7_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 7 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.apply instruction count: 99 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.apply instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.newAggState instruction count: 35 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.setAggState instruction count: 71 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.getAggOffset instruction count: 54 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.ENCODE_o_string_TO_o_binary_11 instruction count: 16 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.bulkStore_12 instruction count: 189 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C7.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 5: (Begin (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) (DeserializeAggs 1 1 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) (CombOp2 0 1 (CollectAsSet () (String) None)) (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None)))) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 5: (Begin (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) (DeserializeAggs 1 1 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None))) (CombOp2 0 1 (CollectAsSet () (String) None)) (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (CollectAsSet () (String) None)))) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_8 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_8_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 8 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.apply instruction count: 270 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.apply instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.insert_5 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.get_6 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.deepCopy_7 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.newAggState instruction count: 53 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.setAggState instruction count: 129 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.getAggOffset instruction count: 103 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.DECODE_o_binary_TO_o_string_14 instruction count: 26 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.bulkLoad_15 instruction count: 381 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.bulkLoad_16 instruction count: 381 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.foreach_17 instruction count: 374 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.ENCODE_o_string_TO_o_binary_18 instruction count: 16 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.bulkStore_19 instruction count: 189 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C8.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: optimize (Compile): before: IR size 5: (Let __iruid_39 (ResultOp2 0 ( (CollectAsSet () (String) None))) (MakeTuple (0) (GetTupleElement 0 (Ref __iruid_39)))) 2019-10-07 18:10:23 root: INFO: optimize (Compile): after: IR size 3: (MakeTuple (0) (GetTupleElement 0 (ResultOp2 0 ( (CollectAsSet () (String) None))))) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_9 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_9_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 9 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9. instruction count: 3 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.apply instruction count: 225 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.apply instruction count: 16 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.method_1 instruction count: 105 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.insert_2 instruction count: 1262 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.get_3 instruction count: 275 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.deepCopy_4 instruction count: 269 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.newAggState instruction count: 35 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.setAggState instruction count: 71 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.getAggOffset instruction count: 54 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.setNumSerialized instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.setSerializedAgg instruction count: 8 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.getSerializedAgg instruction count: 7 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.foreach_11 instruction count: 268 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.setPartitionIndex instruction count: 14 2019-10-07 18:10:23 root: INFO: is/hail/codegen/generated/C9.addPartitionRegion instruction count: 6 2019-10-07 18:10:23 root: INFO: Aggregate: useTreeAggregate=false 2019-10-07 18:10:23 root: INFO: Aggregate: commutative=true 2019-10-07 18:10:23 SparkContext: INFO: Starting job: runJob at RVD.scala:611 2019-10-07 18:10:23 DAGScheduler: INFO: Got job 0 (runJob at RVD.scala:611) with 12 output partitions 2019-10-07 18:10:23 DAGScheduler: INFO: Final stage: ResultStage 0 (runJob at RVD.scala:611) 2019-10-07 18:10:23 DAGScheduler: INFO: Parents of final stage: List() 2019-10-07 18:10:23 DAGScheduler: INFO: Missing parents: List() 2019-10-07 18:10:23 DAGScheduler: INFO: Submitting ResultStage 0 (MapPartitionsRDD[12] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_10 stored as values in memory (estimated size 57.6 KB, free 21.7 GB) 2019-10-07 18:10:23 MemoryStore: INFO: Block broadcast_10_piece0 stored as bytes in memory (estimated size 26.3 KB, free 21.7 GB) 2019-10-07 18:10:23 BlockManagerInfo: INFO: Added broadcast_10_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 26.3 KB, free: 21.7 GB) 2019-10-07 18:10:23 SparkContext: INFO: Created broadcast 10 from broadcast at DAGScheduler.scala:1161 2019-10-07 18:10:24 DAGScheduler: INFO: Submitting 12 missing tasks from ResultStage 0 (MapPartitionsRDD[12] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)) 2019-10-07 18:10:24 YarnScheduler: INFO: Adding task set 0.0 with 12 tasks 2019-10-07 18:10:24 FairSchedulableBuilder: INFO: Added task set TaskSet_0.0 tasks to pool default 2019-10-07 18:10:24 BlockManagerInfo: INFO: Removed broadcast_1_piece0 on mw-m.c.broad-mpg-gnomad.internal:34837 in memory (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 0.0 in stage 0.0 (TID 0, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 0, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 1.0 in stage 0.0 (TID 1, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 1, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 2.0 in stage 0.0 (TID 2, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 2, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 3.0 in stage 0.0 (TID 3, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 3, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 4.0 in stage 0.0 (TID 4, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 4, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 5.0 in stage 0.0 (TID 5, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 5, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 6.0 in stage 0.0 (TID 6, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 6, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 TaskSetManager: INFO: Starting task 7.0 in stage 0.0 (TID 7, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 7, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:24 BlockManagerInfo: INFO: Added broadcast_10_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 26.3 KB, free: 9.5 GB) 2019-10-07 18:10:24 BlockManagerInfo: INFO: Added broadcast_10_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 26.3 KB, free: 9.5 GB) 2019-10-07 18:10:25 ExecutorAllocationManager: INFO: Requesting 1 new executor because tasks are backlogged (new desired total will be 3) 2019-10-07 18:10:25 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:10:25 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:10:26 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 1014.0 B, free: 9.5 GB) 2019-10-07 18:10:26 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 75.0 B, free: 9.5 GB) 2019-10-07 18:10:26 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 1014.0 B, free: 9.5 GB) 2019-10-07 18:10:27 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 75.0 B, free: 9.5 GB) 2019-10-07 18:10:41 TaskSetManager: INFO: Starting task 8.0 in stage 0.0 (TID 8, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:41 TaskSetManager: INFO: Finished task 3.0 in stage 0.0 (TID 3) in 17021 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (1/12) 2019-10-07 18:10:41 root: INFO: RegionPool: initialized for thread 52: dag-scheduler-event-loop 2019-10-07 18:10:41 TaskSetManager: INFO: Starting task 9.0 in stage 0.0 (TID 9, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:41 TaskSetManager: INFO: Finished task 1.0 in stage 0.0 (TID 1) in 17053 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (2/12) 2019-10-07 18:10:41 TaskSetManager: INFO: Starting task 10.0 in stage 0.0 (TID 10, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 10, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:41 TaskSetManager: INFO: Finished task 5.0 in stage 0.0 (TID 5) in 17071 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (3/12) 2019-10-07 18:10:41 TaskSetManager: INFO: Starting task 11.0 in stage 0.0 (TID 11, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 11, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:41 TaskSetManager: INFO: Finished task 7.0 in stage 0.0 (TID 7) in 17162 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (4/12) 2019-10-07 18:10:43 TaskSetManager: INFO: Finished task 0.0 in stage 0.0 (TID 0) in 19190 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (5/12) 2019-10-07 18:10:43 TaskSetManager: INFO: Finished task 2.0 in stage 0.0 (TID 2) in 19203 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (6/12) 2019-10-07 18:10:43 TaskSetManager: INFO: Finished task 4.0 in stage 0.0 (TID 4) in 19243 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (7/12) 2019-10-07 18:10:44 TaskSetManager: INFO: Finished task 6.0 in stage 0.0 (TID 6) in 19956 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (8/12) 2019-10-07 18:10:54 TaskSetManager: INFO: Finished task 9.0 in stage 0.0 (TID 9) in 13487 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (9/12) 2019-10-07 18:10:54 TaskSetManager: INFO: Finished task 11.0 in stage 0.0 (TID 11) in 13388 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (10/12) 2019-10-07 18:10:54 TaskSetManager: INFO: Finished task 10.0 in stage 0.0 (TID 10) in 13530 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (11/12) 2019-10-07 18:10:55 TaskSetManager: INFO: Finished task 8.0 in stage 0.0 (TID 8) in 13879 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (12/12) 2019-10-07 18:10:55 DAGScheduler: INFO: ResultStage 0 (runJob at RVD.scala:611) finished in 31.263 s 2019-10-07 18:10:55 YarnScheduler: INFO: Removed TaskSet 0.0, whose tasks have all completed, from pool default 2019-10-07 18:10:55 DAGScheduler: INFO: Job 0 finished: runJob at RVD.scala:611, took 31.336592 s 2019-10-07 18:10:55 root: INFO: optimize (Compile): before: IR size 3: (MakeTuple (0) (GetField __iruid_38 (Ref __iruid_37))) 2019-10-07 18:10:55 root: INFO: optimize (Compile): after: IR size 3: (MakeTuple (0) (GetField __iruid_38 (Ref __iruid_37))) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_11 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_11_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:55 BlockManagerInfo: INFO: Added broadcast_11_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:55 SparkContext: INFO: Created broadcast 11 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C10. instruction count: 3 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C10.apply instruction count: 76 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C10.apply instruction count: 28 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C10.setPartitionIndex instruction count: 14 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C10.addPartitionRegion instruction count: 6 2019-10-07 18:10:55 root: INFO: Time taken for CompileAndEvaluate -- first pass: 135.425ms 2019-10-07 18:10:55 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 36.542ms 2019-10-07 18:10:55 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 32.138s 2019-10-07 18:10:55 root: INFO: Time taken for CompileAndEvaluate -- compile: 19.451ms 2019-10-07 18:10:55 root: INFO: Time taken for CompileAndEvaluate -- runtime: 3.418ms 2019-10-07 18:10:55 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 268: (TableAggregate (TableFilter (TableMapRows (TableKeyBy (interval) False (TableMapRows (TableFilter (TableMapRows (TableMapRows (TableMapRows (TableRename ("f7" "f6" "f1" "f8" "f0" "f5" "f3" "f4" "f2") ("frame" "strand" "source" "attribute" "seqname" "score" "start" "end" "feature") () () (TableRead None False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (InsertFields (SelectFields (seqname source feature start end score strand frame attribute) (Ref row)) None (attribute (ApplyIR dict Dict[String,String] (ArrayMap __uid_7 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ApplyIR indexArray String (Apply split Array[String] (Ref __uid_7) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ApplyIR indexArray String (Apply split Array[String] (Ref __uid_7) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str "")))))))) (Let __cse_1 (GetField attribute (Ref row)) (SelectFields (seqname source feature start end score strand frame tag transcript_status level gene_id havana_gene gene_type ccdsid exon_number transcript_type exon_id protein_id gene_name transcript_name transcript_id gene_status ont havana_transcript) (InsertFields (SelectFields (seqname source feature start end score strand frame attribute) (Ref row)) None (tag (If (ApplyIR contains Boolean (Ref __cse_1) (Str "tag")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "tag")) (NA String))) (transcript_status (If (ApplyIR contains Boolean (Ref __cse_1) (Str "transcript_status")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "transcript_status")) (NA String))) (level (If (ApplyIR contains Boolean (Ref __cse_1) (Str "level")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "level")) (NA String))) (gene_id (If (ApplyIR contains Boolean (Ref __cse_1) (Str "gene_id")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "gene_id")) (NA String))) (havana_gene (If (ApplyIR contains Boolean (Ref __cse_1) (Str "havana_gene")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "havana_gene")) (NA String))) (gene_type (If (ApplyIR contains Boolean (Ref __cse_1) (Str "gene_type")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "gene_type")) (NA String))) (ccdsid (If (ApplyIR contains Boolean (Ref __cse_1) (Str "ccdsid")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "ccdsid")) (NA String))) (exon_number (If (ApplyIR contains Boolean (Ref __cse_1) (Str "exon_number")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "exon_number")) (NA String))) (transcript_type (If (ApplyIR contains Boolean (Ref __cse_1) (Str "transcript_type")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "transcript_type")) (NA String))) (exon_id (If (ApplyIR contains Boolean (Ref __cse_1) (Str "exon_id")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "exon_id")) (NA String))) (protein_id (If (ApplyIR contains Boolean (Ref __cse_1) (Str "protein_id")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "protein_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __cse_1) (Str "gene_name")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "gene_name")) (NA String))) (transcript_name (If (ApplyIR contains Boolean (Ref __cse_1) (Str "transcript_name")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "transcript_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __cse_1) (Str "transcript_id")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "transcript_id")) (NA String))) (gene_status (If (ApplyIR contains Boolean (Ref __cse_1) (Str "gene_status")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "gene_status")) (NA String))) (ont (If (ApplyIR contains Boolean (Ref __cse_1) (Str "ont")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "ont")) (NA String))) (havana_transcript (If (ApplyIR contains Boolean (Ref __cse_1) (Str "havana_transcript")) (ApplyIR `[]` String (GetField attribute (Ref row)) (Str "havana_transcript")) (NA String))))))) (InsertFields (SelectFields (seqname source feature start end score strand frame tag transcript_status level gene_id havana_gene gene_type ccdsid exon_number transcript_type exon_id protein_id gene_name transcript_name transcript_id gene_status ont havana_transcript) (Ref row)) None (seqname (Apply replace String (GetField seqname (Ref row)) (Str "^chr") (Str ""))))) (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False))) (SelectFields (source feature score strand frame tag transcript_status level gene_id havana_gene gene_type ccdsid exon_number transcript_type exon_id protein_id gene_name transcript_name transcript_id gene_status ont havana_transcript interval) (InsertFields (SelectFields (seqname source feature start end score strand frame tag transcript_status level gene_id havana_gene gene_type ccdsid exon_number transcript_type exon_id protein_id gene_name transcript_name transcript_id gene_status ont havana_transcript) (Ref row)) None (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False))))))) (InsertFields (SelectFields (source feature score strand frame tag transcript_status level gene_id havana_gene gene_type ccdsid exon_number transcript_type exon_id protein_id gene_name transcript_name transcript_id gene_status ont havana_transcript interval) (Ref row)) None (gene_id (ApplyIR indexArray String (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ApplyIR indexArray String (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0))))) (Coalesce (ArrayFold __uid_9 __uid_10 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __uid_9) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __uid_10))))) (False))) (ApplyAggOp Collect () None ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'tag' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'transcript_status' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'level' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'havana_gene' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'gene_type' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'ccdsid' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'exon_number' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'transcript_type' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'exon_id' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'protein_id' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'transcript_name' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'gene_status' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'ont' 2019-10-07 18:10:55 root: INFO: Prune: InsertFields: eliminating field 'havana_transcript' 2019-10-07 18:10:55 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 128: (TableAggregate (TableFilter (TableMapRows (TableKeyBy (interval) False (TableMapRows (TableFilter (TableMapRows (TableRename ("f8" "f0" "f3" "f4" "f2") ("attribute" "seqname" "start" "end" "feature") () () (TableRead Table{global:Struct{},key:[],row:Struct{f0:String,f2:String,f3:Int32,f4:Int32,f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (Let __iruid_1242 (ToDict (ArrayMap __iruid_1243 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_1243) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_1243) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str ""))))) (Let __iruid_1244 (SelectFields (seqname feature start end) (Ref row)) (InsertFields (Ref __iruid_1244) ("seqname" "feature" "start" "end" "gene_id" "gene_name" "transcript_id") (gene_id (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "gene_id")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "gene_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "gene_name")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "gene_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "transcript_id")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "transcript_id")) (NA String))) (seqname (Apply replace String (GetField seqname (Ref __iruid_1244)) (Str "^chr") (Str ""))))))) (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False))) (InsertFields (SelectFields (feature gene_id gene_name transcript_id) (Ref row)) ("feature" "gene_id" "gene_name" "transcript_id" "interval") (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False)))))) (InsertFields (Ref row) None (gene_id (ArrayRef (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ArrayRef (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0))))) (Coalesce (ArrayFold __iruid_1269 __iruid_1270 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __iruid_1269) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __iruid_1270))))) (False))) (ApplyAggOp Collect () None ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:10:55 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 128: (TableAggregate (TableFilter (TableMapRows (TableKeyBy (interval) False (TableMapRows (TableFilter (TableMapRows (TableRename ("f8" "f0" "f3" "f4" "f2") ("attribute" "seqname" "start" "end" "feature") () () (TableRead Table{global:Struct{},key:[],row:Struct{f0:String,f2:String,f3:Int32,f4:Int32,f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (Let __iruid_1242 (ToDict (ArrayMap __iruid_1243 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_1243) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_1243) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str ""))))) (Let __iruid_1244 (SelectFields (seqname feature start end) (Ref row)) (InsertFields (Ref __iruid_1244) ("seqname" "feature" "start" "end" "gene_id" "gene_name" "transcript_id") (gene_id (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "gene_id")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "gene_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "gene_name")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "gene_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __iruid_1242) (Str "transcript_id")) (ApplyIR `[]` String (Ref __iruid_1242) (Str "transcript_id")) (NA String))) (seqname (Apply replace String (GetField seqname (Ref __iruid_1244)) (Str "^chr") (Str ""))))))) (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False))) (InsertFields (SelectFields (feature gene_id gene_name transcript_id) (Ref row)) ("feature" "gene_id" "gene_name" "transcript_id" "interval") (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False)))))) (InsertFields (Ref row) None (gene_id (ArrayRef (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ArrayRef (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0))))) (Coalesce (ArrayFold __iruid_1269 __iruid_1270 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __iruid_1269) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __iruid_1270))))) (False))) (ApplyAggOp Collect () None ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:10:55 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 128: (TableAggregate (TableFilter (TableMapRows (TableKeyBy (interval) False (TableMapRows (TableFilter (TableMapRows (TableRename ("f8" "f0" "f3" "f4" "f2") ("attribute" "seqname" "start" "end" "feature") () () (TableRead Table{global:Struct{},key:[],row:Struct{f0:String,f2:String,f3:Int32,f4:Int32,f8:String}} False "{\"name\":\"TextTableReader\",\"options\":{\"files\":[\"gs://hail-common/references/gencode/gencode.v19.annotation.gtf.bgz\"],\"typeMapStr\":{\"f3\":\"Int32\",\"f4\":\"Int32\",\"f5\":\"Float64\",\"f7\":\"Int32\"},\"comment\":[\"#\"],\"separator\":\"\\t\",\"missing\":[\".\"],\"noHeader\":true,\"impute\":false,\"nPartitionsOpt\":12,\"quoteStr\":null,\"skipBlankLines\":false,\"forceBGZ\":false,\"filterAndReplace\":{\"name\":\"TextInputFilterAndReplace\"},\"forceGZ\":false}}")) (Let __iruid_1572 (ToDict (ArrayMap __iruid_1573 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_1573) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_1573) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str ""))))) (Let __iruid_1574 (SelectFields (seqname feature start end) (Ref row)) (InsertFields (Ref __iruid_1574) ("seqname" "feature" "start" "end" "gene_id" "gene_name" "transcript_id") (gene_id (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "gene_id")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "gene_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "gene_name")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "gene_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "transcript_id")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "transcript_id")) (NA String))) (seqname (Apply replace String (GetField seqname (Ref __iruid_1574)) (Str "^chr") (Str ""))))))) (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False))) (InsertFields (SelectFields (feature gene_id gene_name transcript_id) (Ref row)) ("feature" "gene_id" "gene_name" "transcript_id" "interval") (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False)))))) (InsertFields (Ref row) None (gene_id (ArrayRef (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ArrayRef (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0))))) (Coalesce (ArrayFold __iruid_1599 __iruid_1600 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __iruid_1599) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __iruid_1600))))) (False))) (ApplyAggOp Collect () None ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_12 stored as values in memory (estimated size 401.3 KB, free 21.7 GB) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_12_piece0 stored as bytes in memory (estimated size 28.2 KB, free 21.7 GB) 2019-10-07 18:10:55 BlockManagerInfo: INFO: Added broadcast_12_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:10:55 SparkContext: INFO: Created broadcast 12 from textFile at RichSparkContext.scala:16 2019-10-07 18:10:55 FileInputFormat: INFO: Total input files to process : 1 2019-10-07 18:10:55 root: INFO: couldn't lower TableMapRows: is.hail.expr.ir.agg.UnsupportedExtraction: no scans to extract in TableMapRows 2019-10-07 18:10:55 root: INFO: initop (Begin) 2019-10-07 18:10:55 root: INFO: optimize (Compile): before: IR size 1: (Begin) 2019-10-07 18:10:55 root: INFO: optimize (Compile): after: IR size 1: (Begin) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_13 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_13_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:55 BlockManagerInfo: INFO: Added broadcast_13_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:55 SparkContext: INFO: Created broadcast 13 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C11. instruction count: 3 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C11.apply instruction count: 15 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C11.apply instruction count: 16 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C11.setPartitionIndex instruction count: 14 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C11.addPartitionRegion instruction count: 6 2019-10-07 18:10:55 root: INFO: seqop (Begin) 2019-10-07 18:10:55 root: INFO: optimize (Compile): before: IR size 1: (Begin) 2019-10-07 18:10:55 root: INFO: optimize (Compile): after: IR size 1: (Begin) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_14 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:55 MemoryStore: INFO: Block broadcast_14_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:55 BlockManagerInfo: INFO: Added broadcast_14_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:55 SparkContext: INFO: Created broadcast 14 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C12. instruction count: 3 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C12.apply instruction count: 15 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C12.apply instruction count: 22 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C12.setPartitionIndex instruction count: 14 2019-10-07 18:10:55 root: INFO: is/hail/codegen/generated/C12.addPartitionRegion instruction count: 6 2019-10-07 18:10:55 root: INFO: optimize (Compile): before: IR size 58: (Let __iruid_1572 (ToDict (ArrayMap __iruid_1573 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_1573) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_1573) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str ""))))) (Let __iruid_1574 (SelectFields (seqname feature start end) (Ref row)) (InsertFields (Ref __iruid_1574) ("seqname" "feature" "start" "end" "gene_id" "gene_name" "transcript_id") (gene_id (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "gene_id")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "gene_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "gene_name")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "gene_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __iruid_1572) (Str "transcript_id")) (ApplyIR `[]` String (Ref __iruid_1572) (Str "transcript_id")) (NA String))) (seqname (Apply replace String (GetField seqname (Ref __iruid_1574)) (Str "^chr") (Str "")))))) 2019-10-07 18:10:55 root: INFO: optimize (Compile): after: IR size 58: (Let __iruid_1985 (ToDict (ArrayMap __iruid_1986 (Apply split Array[String] (GetField attribute (Ref row)) (Str "; ")) (MakeTuple (0 1) (ArrayRef (Apply split Array[String] (Ref __iruid_1986) (Str " ")) (I32 0)) (Apply replace String (Apply replace String (ArrayRef (Apply split Array[String] (Ref __iruid_1986) (Str " ")) (I32 1)) (Str "\"") (Str "")) (Str ";$") (Str ""))))) (Let __iruid_1987 (SelectFields (seqname feature start end) (Ref row)) (InsertFields (Ref __iruid_1987) ("seqname" "feature" "start" "end" "gene_id" "gene_name" "transcript_id") (gene_id (If (ApplyIR contains Boolean (Ref __iruid_1985) (Str "gene_id")) (ApplyIR `[]` String (Ref __iruid_1985) (Str "gene_id")) (NA String))) (gene_name (If (ApplyIR contains Boolean (Ref __iruid_1985) (Str "gene_name")) (ApplyIR `[]` String (Ref __iruid_1985) (Str "gene_name")) (NA String))) (transcript_id (If (ApplyIR contains Boolean (Ref __iruid_1985) (Str "transcript_id")) (ApplyIR `[]` String (Ref __iruid_1985) (Str "transcript_id")) (NA String))) (seqname (Apply replace String (GetField seqname (Ref __iruid_1987)) (Str "^chr") (Str "")))))) 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14.apply instruction count: 11 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14.apply instruction count: 14 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14.method_1 instruction count: 114 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14.method_2 instruction count: 45 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C14.method_3 instruction count: 105 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_15. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_15.apply instruction count: 7 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_15.apply instruction count: 11 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_15.ENCODE_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringEND_TO_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryEND_1 instruction count: 205 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_15.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_15 stored as values in memory (estimated size 192.0 B, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_15_piece0 stored as bytes in memory (estimated size 175.0 B, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_15_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 175.0 B, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 15 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.apply instruction count: 1123 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.apply instruction count: 28 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_1 instruction count: 103 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_2 instruction count: 106 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_3 instruction count: 329 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_4 instruction count: 150 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_5 instruction count: 33 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_6 instruction count: 150 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_7 instruction count: 423 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_8 instruction count: 33 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_9 instruction count: 349 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_10 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_11 instruction count: 105 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_12 instruction count: 37 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_13 instruction count: 660 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_14 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_15 instruction count: 29 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_16 instruction count: 42 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_17 instruction count: 60 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_18 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_19 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_20 instruction count: 349 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_21 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_22 instruction count: 660 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_23 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_24 instruction count: 29 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_25 instruction count: 42 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_26 instruction count: 60 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_27 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_28 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_29 instruction count: 349 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_30 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_31 instruction count: 660 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_32 instruction count: 89 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_33 instruction count: 29 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_34 instruction count: 42 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_35 instruction count: 60 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_36 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.method_37 instruction count: 224 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.setPartitionIndex instruction count: 14 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.addPartitionRegion instruction count: 6 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.DECODE_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_binaryEND_TO_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringANDo_stringEND_40 instruction count: 303 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.INPLACE_DECODE_o_binary_TO_o_binary_41 instruction count: 29 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C13.addLiterals instruction count: 100 2019-10-07 18:10:56 root: INFO: optimize (Compile): before: IR size 6: (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False)) 2019-10-07 18:10:56 root: INFO: optimize (Compile): after: IR size 6: (Coalesce (ApplyIR contains Boolean (Literal Set[String] ) (GetField seqname (Ref row))) (False)) 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17.apply instruction count: 7 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17.apply instruction count: 11 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17.ENCODE_o_tuple_of_o_set_of_o_stringEND_TO_o_struct_of_o_array_of_o_binaryEND_1 instruction count: 25 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17.ENCODE_o_array_of_o_binary_TO_o_array_of_o_binary_2 instruction count: 78 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_17.ENCODE_o_binary_TO_o_binary_3 instruction count: 16 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_16 stored as values in memory (estimated size 1048.0 B, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_16_piece0 stored as bytes in memory (estimated size 422.0 B, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_16_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 422.0 B, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 16 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.apply instruction count: 51 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.apply instruction count: 22 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.method_1 instruction count: 366 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.method_2 instruction count: 105 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.method_3 instruction count: 106 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.method_4 instruction count: 80 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.method_5 instruction count: 37 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.setPartitionIndex instruction count: 14 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.addPartitionRegion instruction count: 6 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.DECODE_o_struct_of_o_array_of_o_binaryEND_TO_o_tuple_of_o_set_of_o_stringEND_8 instruction count: 46 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.INPLACE_DECODE_o_array_of_o_binary_TO_o_array_of_o_binary_9 instruction count: 99 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.INPLACE_DECODE_o_binary_TO_o_binary_10 instruction count: 29 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C16.addLiterals instruction count: 30 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_18. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.apply instruction count: 7 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.apply instruction count: 11 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.ENCODE_o_tuple_of_END_TO_o_struct_of_END_1 instruction count: 7 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeDecode_19. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.apply instruction count: 7 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.apply instruction count: 12 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.DECODE_o_struct_of_END_TO_o_tuple_of_END_1 instruction count: 14 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_17 stored as values in memory (estimated size 2.8 KB, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_17_piece0 stored as bytes in memory (estimated size 1015.0 B, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_17_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 1015.0 B, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 17 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:56 root: INFO: couldn't lower TableMapRows: is.hail.expr.ir.agg.UnsupportedExtraction: no scans to extract in TableMapRows 2019-10-07 18:10:56 root: INFO: initop (Begin) 2019-10-07 18:10:56 root: INFO: seqop (Begin) 2019-10-07 18:10:56 root: INFO: optimize (Compile): before: IR size 1: (Begin) 2019-10-07 18:10:56 root: INFO: optimize (Compile): after: IR size 1: (Begin) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_18 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_18_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_18_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 18 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C20. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C20.apply instruction count: 15 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C20.apply instruction count: 22 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C20.setPartitionIndex instruction count: 14 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C20.addPartitionRegion instruction count: 6 2019-10-07 18:10:56 root: INFO: optimize (Compile): before: IR size 13: (InsertFields (SelectFields (feature gene_id gene_name transcript_id) (Ref row)) ("feature" "gene_id" "gene_name" "transcript_id" "interval") (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False)))) 2019-10-07 18:10:56 root: INFO: optimize (Compile): after: IR size 13: (InsertFields (SelectFields (feature gene_id gene_name transcript_id) (Ref row)) ("feature" "gene_id" "gene_name" "transcript_id" "interval") (interval (ApplySpecial LocusInterval Interval[Locus(GRCh37)] (GetField seqname (Ref row)) (GetField start (Ref row)) (GetField end (Ref row)) (True) (True) (False)))) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_19 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_19_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_19_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 19 from broadcast at SparkBackend.scala:21 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21. instruction count: 3 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21.apply instruction count: 193 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21.apply instruction count: 28 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21.method_1 instruction count: 490 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21.setPartitionIndex instruction count: 14 2019-10-07 18:10:56 root: INFO: is/hail/codegen/generated/C21.addPartitionRegion instruction count: 6 2019-10-07 18:10:56 SparkContext: INFO: Starting job: collect at ContextRDD.scala:222 2019-10-07 18:10:56 DAGScheduler: INFO: Got job 1 (collect at ContextRDD.scala:222) with 12 output partitions 2019-10-07 18:10:56 DAGScheduler: INFO: Final stage: ResultStage 1 (collect at ContextRDD.scala:222) 2019-10-07 18:10:56 DAGScheduler: INFO: Parents of final stage: List() 2019-10-07 18:10:56 DAGScheduler: INFO: Missing parents: List() 2019-10-07 18:10:56 DAGScheduler: INFO: Submitting ResultStage 1 (MapPartitionsRDD[25] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_20 stored as values in memory (estimated size 89.4 KB, free 21.7 GB) 2019-10-07 18:10:56 MemoryStore: INFO: Block broadcast_20_piece0 stored as bytes in memory (estimated size 38.0 KB, free 21.7 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_20_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 38.0 KB, free: 21.7 GB) 2019-10-07 18:10:56 SparkContext: INFO: Created broadcast 20 from broadcast at DAGScheduler.scala:1161 2019-10-07 18:10:56 DAGScheduler: INFO: Submitting 12 missing tasks from ResultStage 1 (MapPartitionsRDD[25] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)) 2019-10-07 18:10:56 YarnScheduler: INFO: Adding task set 1.0 with 12 tasks 2019-10-07 18:10:56 FairSchedulableBuilder: INFO: Added task set TaskSet_1.0 tasks to pool default 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 0.0 in stage 1.0 (TID 12, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 0, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 1.0 in stage 1.0 (TID 13, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 1, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 2.0 in stage 1.0 (TID 14, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 2, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 3.0 in stage 1.0 (TID 15, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 3, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 4.0 in stage 1.0 (TID 16, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 4, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 5.0 in stage 1.0 (TID 17, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 5, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 6.0 in stage 1.0 (TID 18, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 6, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 TaskSetManager: INFO: Starting task 7.0 in stage 1.0 (TID 19, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 7, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_20_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 38.0 KB, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_20_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 38.0 KB, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_12_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_12_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_16_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 422.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_17_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 1015.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_16_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 422.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_17_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 1015.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_15_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 175.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_15_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 175.0 B, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 2.9 KB, free: 9.5 GB) 2019-10-07 18:10:56 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 2.9 KB, free: 9.5 GB) 2019-10-07 18:10:57 ExecutorAllocationManager: INFO: Requesting 2 new executors because tasks are backlogged (new desired total will be 3) 2019-10-07 18:11:11 TaskSetManager: INFO: Starting task 8.0 in stage 1.0 (TID 20, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:11:11 TaskSetManager: INFO: Finished task 3.0 in stage 1.0 (TID 15) in 15191 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (1/12) 2019-10-07 18:11:11 TaskSetManager: INFO: Starting task 9.0 in stage 1.0 (TID 21, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:11:11 TaskSetManager: INFO: Finished task 5.0 in stage 1.0 (TID 17) in 15312 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (2/12) 2019-10-07 18:11:11 TaskSetManager: INFO: Starting task 10.0 in stage 1.0 (TID 22, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 10, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:11:11 TaskSetManager: INFO: Finished task 1.0 in stage 1.0 (TID 13) in 15529 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (3/12) 2019-10-07 18:11:11 TaskSetManager: INFO: Starting task 11.0 in stage 1.0 (TID 23, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 11, PROCESS_LOCAL, 7937 bytes) 2019-10-07 18:11:11 TaskSetManager: INFO: Finished task 7.0 in stage 1.0 (TID 19) in 15540 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (4/12) 2019-10-07 18:11:12 TaskSetManager: INFO: Finished task 4.0 in stage 1.0 (TID 16) in 16299 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (5/12) 2019-10-07 18:11:12 TaskSetManager: INFO: Finished task 0.0 in stage 1.0 (TID 12) in 16592 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (6/12) 2019-10-07 18:11:12 TaskSetManager: INFO: Finished task 6.0 in stage 1.0 (TID 18) in 16670 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (7/12) 2019-10-07 18:11:13 TaskSetManager: INFO: Finished task 2.0 in stage 1.0 (TID 14) in 16809 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (8/12) 2019-10-07 18:11:25 TaskSetManager: INFO: Finished task 8.0 in stage 1.0 (TID 20) in 14536 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (9/12) 2019-10-07 18:11:26 TaskSetManager: INFO: Finished task 9.0 in stage 1.0 (TID 21) in 14631 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (10/12) 2019-10-07 18:11:26 TaskSetManager: INFO: Finished task 11.0 in stage 1.0 (TID 23) in 14519 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (11/12) 2019-10-07 18:11:26 TaskSetManager: INFO: Finished task 10.0 in stage 1.0 (TID 22) in 14822 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (12/12) 2019-10-07 18:11:26 YarnScheduler: INFO: Removed TaskSet 1.0, whose tasks have all completed, from pool default 2019-10-07 18:11:26 DAGScheduler: INFO: ResultStage 1 (collect at ContextRDD.scala:222) finished in 30.359 s 2019-10-07 18:11:26 DAGScheduler: INFO: Job 1 finished: collect at ContextRDD.scala:222, took 30.363930 s 2019-10-07 18:11:26 Hail: INFO: Ordering unsorted dataset with network shuffle 2019-10-07 18:11:26 root: INFO: Unsorted keys: CURRENT={ interval: { start: { contig: 1, position: 11869 }, end: { contig: 1, position: 14409 }, includesStart: true, includesEnd: true } }, PREV={ interval: { start: { contig: 1, position: 11869 }, end: { contig: 1, position: 14412 }, includesStart: true, includesEnd: true } } 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_21 stored as values in memory (estimated size 72.3 KB, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_21_piece0 stored as bytes in memory (estimated size 1592.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_21_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 1592.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 21 from broadcast at RVDPartitioner.scala:87 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.apply instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.apply instruction count: 11 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_interval_of_o_locusEND_TO_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_1 instruction count: 95 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_3 instruction count: 69 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_o_tuple_of_r_binaryANDr_int32END_TO_o_struct_of_r_binaryANDr_int32END_4 instruction count: 37 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_r_binary_TO_r_binary_5 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_r_int32_TO_r_int32_6 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_22.ENCODE_r_bool_TO_r_bool_7 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.apply instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.apply instruction count: 12 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.DECODE_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_interval_of_o_locusEND_1 instruction count: 146 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_3 instruction count: 79 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_4 instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_r_binary_TO_r_binary_5 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_r_int32_TO_r_int32_6 instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_r_bool_TO_r_bool_7 instruction count: 8 2019-10-07 18:11:26 root: INFO: couldn't lower TableMapRows: is.hail.expr.ir.agg.UnsupportedExtraction: no scans to extract in TableMapRows 2019-10-07 18:11:26 root: INFO: initop (Begin) 2019-10-07 18:11:26 root: INFO: seqop (Begin) 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 1: (Begin) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 1: (Begin) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_22 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_22_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_22_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 22 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C24. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C24.apply instruction count: 15 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C24.apply instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C24.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C24.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 14: (InsertFields (Ref row) None (gene_id (ArrayRef (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ArrayRef (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0)))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 14: (InsertFields (Ref row) None (gene_id (ArrayRef (Apply split Array[String] (GetField gene_id (Ref row)) (Str "\\.")) (I32 0))) (transcript_id (ArrayRef (Apply split Array[String] (GetField transcript_id (Ref row)) (Str "\\.")) (I32 0)))) 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_26. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_26.apply instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_26.apply instruction count: 11 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_26.ENCODE_o_tuple_of_o_stringEND_TO_o_struct_of_o_binaryEND_1 instruction count: 25 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_26.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_23 stored as values in memory (estimated size 72.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_23_piece0 stored as bytes in memory (estimated size 60.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_23_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 60.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 23 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.apply instruction count: 48 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.apply instruction count: 28 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.method_1 instruction count: 424 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.method_2 instruction count: 150 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_5 instruction count: 46 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.INPLACE_DECODE_o_binary_TO_o_binary_6 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C25.addLiterals instruction count: 30 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 16: (Coalesce (ArrayFold __iruid_1599 __iruid_1600 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __iruid_1599) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __iruid_1600))))) (False)) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 16: (Coalesce (ArrayFold __iruid_2093 __iruid_2094 (Literal Array[String] ) (False) (ApplySpecial `||` Boolean (Ref __iruid_2093) (ApplySpecial `&&` Boolean (ApplyComparisonOp EQ (GetField feature (Ref row)) (Str "gene")) (ApplyComparisonOp EQ (GetField gene_name (Ref row)) (Ref __iruid_2094))))) (False)) 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28.apply instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28.apply instruction count: 11 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28.ENCODE_o_tuple_of_o_array_of_o_stringANDo_stringEND_TO_o_struct_of_o_array_of_o_binaryANDo_binaryEND_1 instruction count: 43 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28.ENCODE_o_array_of_o_binary_TO_o_array_of_o_binary_2 instruction count: 78 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C_etypeEncode_28.ENCODE_o_binary_TO_o_binary_3 instruction count: 16 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_24 stored as values in memory (estimated size 120.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_24_piece0 stored as bytes in memory (estimated size 100.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_24_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 100.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 24 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.apply instruction count: 591 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.apply instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.method_1 instruction count: 106 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.DECODE_o_struct_of_o_array_of_o_binaryANDo_binaryEND_TO_o_tuple_of_o_array_of_o_stringANDo_stringEND_4 instruction count: 71 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.INPLACE_DECODE_o_array_of_o_binary_TO_o_array_of_o_binary_5 instruction count: 99 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.INPLACE_DECODE_o_binary_TO_o_binary_6 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C27.addLiterals instruction count: 37 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 2: (Begin (InitOp2 0 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None) ())) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 2: (Begin (InitOp2 0 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None) ())) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_25 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_25_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_25_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 25 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.apply instruction count: 100 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.apply instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.newAggState instruction count: 36 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.setAggState instruction count: 67 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.getAggOffset instruction count: 53 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C29.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 13: (Begin (SeqOp2 0 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None) ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 13: (Begin (SeqOp2 0 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None) ( (MakeTuple (0 1 2 3 4) (GetField feature (Ref row)) (GetField gene_name (Ref row)) (GetField gene_id (Ref row)) (GetField transcript_id (Ref row)) (GetField interval (Ref row)))))) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_26 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_26_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_26_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 26 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.apply instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.apply instruction count: 20 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.newAggState instruction count: 36 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.setAggState instruction count: 67 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.getAggOffset instruction count: 53 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.method_7 instruction count: 49 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.method_8 instruction count: 226 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.blockLinkedListPush_9 instruction count: 919 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C30.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 1: (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 1: (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_27 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_27_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_27_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 27 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.apply instruction count: 122 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.apply instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.newAggState instruction count: 36 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.setAggState instruction count: 67 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.getAggOffset instruction count: 53 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.blockLinkedListDeserialize_7 instruction count: 60 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.DECODE_r_array_of_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_array_of_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_interval_of_o_locusEND_8 instruction count: 96 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_tuple_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_9 instruction count: 140 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_o_binary_TO_o_binary_10 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_11 instruction count: 79 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_12 instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_r_binary_TO_r_binary_13 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_r_int32_TO_r_int32_14 instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.INPLACE_DECODE_r_bool_TO_r_bool_15 instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C31.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 1: (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 1: (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_28 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_28_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_28_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 28 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.apply instruction count: 98 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.apply instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.newAggState instruction count: 36 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.setAggState instruction count: 67 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.getAggOffset instruction count: 53 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.blockLinkedListSerialize_7 instruction count: 136 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_o_tuple_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_8 instruction count: 95 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_o_binary_TO_o_binary_9 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_10 instruction count: 69 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_o_tuple_of_r_binaryANDr_int32END_TO_o_struct_of_r_binaryANDr_int32END_11 instruction count: 37 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_r_binary_TO_r_binary_12 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_r_int32_TO_r_int32_13 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.ENCODE_r_bool_TO_r_bool_14 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C32.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 5: (Begin (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) (DeserializeAggs 1 1 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) (CombOp2 0 1 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None)) (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None)))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 5: (Begin (DeserializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) (DeserializeAggs 1 1 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) (CombOp2 0 1 (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None)) (SerializeAggs 0 0 "{\"name\":\"BlockingBufferSpec\",\"blockSize\":32768,\"child\":{\"name\":\"StreamBlockBufferSpec\"}}" ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None)))) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_29 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_29_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_29_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 29 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.apply instruction count: 364 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.apply instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.newAggState instruction count: 55 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.setAggState instruction count: 121 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.getAggOffset instruction count: 101 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.blockLinkedListDeserialize_7 instruction count: 60 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.DECODE_r_array_of_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_r_array_of_o_tuple_of_o_stringANDo_stringANDo_stringANDo_stringANDo_interval_of_o_locusEND_8 instruction count: 96 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_tuple_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_9 instruction count: 140 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_o_binary_TO_o_binary_10 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_11 instruction count: 79 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_12 instruction count: 22 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_r_binary_TO_r_binary_13 instruction count: 29 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_r_int32_TO_r_int32_14 instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.INPLACE_DECODE_r_bool_TO_r_bool_15 instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.blockLinkedListDeserialize_16 instruction count: 60 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.blockLinkedListAppend_17 instruction count: 1012 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.blockLinkedListSerialize_18 instruction count: 136 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_o_tuple_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_struct_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_19 instruction count: 95 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_o_binary_TO_o_binary_20 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_21 instruction count: 69 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_o_tuple_of_r_binaryANDr_int32END_TO_o_struct_of_r_binaryANDr_int32END_22 instruction count: 37 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_r_binary_TO_r_binary_23 instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_r_int32_TO_r_int32_24 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.ENCODE_r_bool_TO_r_bool_25 instruction count: 6 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C33.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: optimize (Compile): before: IR size 5: (Let __iruid_2095 (ResultOp2 0 ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))) (MakeTuple (0) (GetTupleElement 0 (Ref __iruid_2095)))) 2019-10-07 18:11:26 root: INFO: optimize (Compile): after: IR size 3: (MakeTuple (0) (GetTupleElement 0 (ResultOp2 0 ( (Collect () (Tuple[String,String,String,String,Interval[Locus(GRCh37)]]) None))))) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_30 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_30_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_30_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 30 from broadcast at SparkBackend.scala:21 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34. instruction count: 3 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.apply instruction count: 140 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.apply instruction count: 16 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.newAggState instruction count: 36 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.setAggState instruction count: 67 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.getAggOffset instruction count: 53 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.setNumSerialized instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.setSerializedAgg instruction count: 8 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.getSerializedAgg instruction count: 7 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.blockLinkedListToSRVB_7 instruction count: 575 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.setPartitionIndex instruction count: 14 2019-10-07 18:11:26 root: INFO: is/hail/codegen/generated/C34.addPartitionRegion instruction count: 6 2019-10-07 18:11:26 root: INFO: Aggregate: useTreeAggregate=false 2019-10-07 18:11:26 root: INFO: Aggregate: commutative=false 2019-10-07 18:11:26 SparkContext: INFO: Starting job: runJob at RVD.scala:611 2019-10-07 18:11:26 DAGScheduler: INFO: Registering RDD 28 (mapPartitions at ContextRDD.scala:216) 2019-10-07 18:11:26 DAGScheduler: INFO: Got job 2 (runJob at RVD.scala:611) with 12 output partitions 2019-10-07 18:11:26 DAGScheduler: INFO: Final stage: ResultStage 3 (runJob at RVD.scala:611) 2019-10-07 18:11:26 DAGScheduler: INFO: Parents of final stage: List(ShuffleMapStage 2) 2019-10-07 18:11:26 DAGScheduler: INFO: Missing parents: List(ShuffleMapStage 2) 2019-10-07 18:11:26 DAGScheduler: INFO: Submitting ShuffleMapStage 2 (MapPartitionsRDD[28] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_31 stored as values in memory (estimated size 96.6 KB, free 21.7 GB) 2019-10-07 18:11:26 MemoryStore: INFO: Block broadcast_31_piece0 stored as bytes in memory (estimated size 41.6 KB, free 21.7 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_31_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 41.6 KB, free: 21.7 GB) 2019-10-07 18:11:26 SparkContext: INFO: Created broadcast 31 from broadcast at DAGScheduler.scala:1161 2019-10-07 18:11:26 DAGScheduler: INFO: Submitting 12 missing tasks from ShuffleMapStage 2 (MapPartitionsRDD[28] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)) 2019-10-07 18:11:26 YarnScheduler: INFO: Adding task set 2.0 with 12 tasks 2019-10-07 18:11:26 FairSchedulableBuilder: INFO: Added task set TaskSet_2.0 tasks to pool default 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 0.0 in stage 2.0 (TID 24, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 0, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 1.0 in stage 2.0 (TID 25, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 1, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 2.0 in stage 2.0 (TID 26, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 2, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 3.0 in stage 2.0 (TID 27, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 3, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 4.0 in stage 2.0 (TID 28, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 4, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 5.0 in stage 2.0 (TID 29, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 5, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 6.0 in stage 2.0 (TID 30, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 6, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 TaskSetManager: INFO: Starting task 7.0 in stage 2.0 (TID 31, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 7, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_31_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 41.6 KB, free: 9.5 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_31_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 41.6 KB, free: 9.5 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_21_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 1592.0 B, free: 9.5 GB) 2019-10-07 18:11:26 BlockManagerInfo: INFO: Added broadcast_21_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 1592.0 B, free: 9.5 GB) 2019-10-07 18:11:27 ExecutorAllocationManager: INFO: Requesting 2 new executors because tasks are backlogged (new desired total will be 3) 2019-10-07 18:11:45 TaskSetManager: INFO: Starting task 8.0 in stage 2.0 (TID 32, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:45 TaskSetManager: INFO: Finished task 3.0 in stage 2.0 (TID 27) in 18776 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (1/12) 2019-10-07 18:11:45 TaskSetManager: INFO: Starting task 9.0 in stage 2.0 (TID 33, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:45 TaskSetManager: INFO: Finished task 5.0 in stage 2.0 (TID 29) in 18881 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (2/12) 2019-10-07 18:11:45 TaskSetManager: INFO: Starting task 10.0 in stage 2.0 (TID 34, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 10, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:45 TaskSetManager: INFO: Finished task 1.0 in stage 2.0 (TID 25) in 18909 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (3/12) 2019-10-07 18:11:45 TaskSetManager: INFO: Starting task 11.0 in stage 2.0 (TID 35, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 11, PROCESS_LOCAL, 7926 bytes) 2019-10-07 18:11:45 TaskSetManager: INFO: Finished task 7.0 in stage 2.0 (TID 31) in 18962 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (4/12) 2019-10-07 18:11:47 TaskSetManager: INFO: Finished task 4.0 in stage 2.0 (TID 28) in 20330 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (5/12) 2019-10-07 18:11:47 TaskSetManager: INFO: Finished task 2.0 in stage 2.0 (TID 26) in 20517 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (6/12) 2019-10-07 18:11:47 TaskSetManager: INFO: Finished task 6.0 in stage 2.0 (TID 30) in 21078 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (7/12) 2019-10-07 18:11:47 TaskSetManager: INFO: Finished task 0.0 in stage 2.0 (TID 24) in 21119 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (8/12) 2019-10-07 18:12:04 TaskSetManager: INFO: Finished task 8.0 in stage 2.0 (TID 32) in 18580 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (9/12) 2019-10-07 18:12:04 TaskSetManager: INFO: Finished task 11.0 in stage 2.0 (TID 35) in 18543 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (10/12) 2019-10-07 18:12:04 TaskSetManager: INFO: Finished task 9.0 in stage 2.0 (TID 33) in 18643 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (11/12) 2019-10-07 18:12:04 TaskSetManager: INFO: Finished task 10.0 in stage 2.0 (TID 34) in 18793 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (12/12) 2019-10-07 18:12:04 YarnScheduler: INFO: Removed TaskSet 2.0, whose tasks have all completed, from pool default 2019-10-07 18:12:04 DAGScheduler: INFO: ShuffleMapStage 2 (mapPartitions at ContextRDD.scala:216) finished in 37.716 s 2019-10-07 18:12:04 DAGScheduler: INFO: looking for newly runnable stages 2019-10-07 18:12:04 DAGScheduler: INFO: running: Set() 2019-10-07 18:12:04 DAGScheduler: INFO: waiting: Set(ResultStage 3) 2019-10-07 18:12:04 DAGScheduler: INFO: failed: Set() 2019-10-07 18:12:04 DAGScheduler: INFO: Submitting ResultStage 3 (MapPartitionsRDD[36] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-07 18:12:04 MemoryStore: INFO: Block broadcast_32 stored as values in memory (estimated size 49.1 KB, free 21.7 GB) 2019-10-07 18:12:04 MemoryStore: INFO: Block broadcast_32_piece0 stored as bytes in memory (estimated size 23.6 KB, free 21.7 GB) 2019-10-07 18:12:04 BlockManagerInfo: INFO: Added broadcast_32_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 23.6 KB, free: 21.7 GB) 2019-10-07 18:12:04 SparkContext: INFO: Created broadcast 32 from broadcast at DAGScheduler.scala:1161 2019-10-07 18:12:04 DAGScheduler: INFO: Submitting 12 missing tasks from ResultStage 3 (MapPartitionsRDD[36] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11)) 2019-10-07 18:12:04 YarnScheduler: INFO: Adding task set 3.0 with 12 tasks 2019-10-07 18:12:04 FairSchedulableBuilder: INFO: Added task set TaskSet_3.0 tasks to pool default 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 0.0 in stage 3.0 (TID 36, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 0, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 1.0 in stage 3.0 (TID 37, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 1, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 2.0 in stage 3.0 (TID 38, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 2, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 3.0 in stage 3.0 (TID 39, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 3, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 4.0 in stage 3.0 (TID 40, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 4, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 5.0 in stage 3.0 (TID 41, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 5, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 6.0 in stage 3.0 (TID 42, mw-w-1.c.broad-mpg-gnomad.internal, executor 2, partition 6, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 TaskSetManager: INFO: Starting task 7.0 in stage 3.0 (TID 43, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 7, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:04 BlockManagerInfo: INFO: Added broadcast_32_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 23.6 KB, free: 9.5 GB) 2019-10-07 18:12:04 BlockManagerInfo: INFO: Added broadcast_32_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 23.6 KB, free: 9.5 GB) 2019-10-07 18:12:04 MapOutputTrackerMasterEndpoint: INFO: Asked to send map output locations for shuffle 0 to 10.128.0.5:54000 2019-10-07 18:12:04 MapOutputTrackerMasterEndpoint: INFO: Asked to send map output locations for shuffle 0 to 10.128.0.10:46280 2019-10-07 18:12:05 ExecutorAllocationManager: INFO: Requesting 2 new executors because tasks are backlogged (new desired total will be 3) 2019-10-07 18:12:05 BlockManagerInfo: INFO: Added broadcast_24_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 100.0 B, free: 9.5 GB) 2019-10-07 18:12:05 BlockManagerInfo: INFO: Added broadcast_23_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:37157 (size: 60.0 B, free: 9.5 GB) 2019-10-07 18:12:05 BlockManagerInfo: INFO: Added broadcast_24_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 100.0 B, free: 9.5 GB) 2019-10-07 18:12:06 BlockManagerInfo: INFO: Added broadcast_23_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:39849 (size: 60.0 B, free: 9.5 GB) 2019-10-07 18:12:06 TaskSetManager: INFO: Starting task 8.0 in stage 3.0 (TID 44, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 8, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 7.0 in stage 3.0 (TID 43) in 2143 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (1/12) 2019-10-07 18:12:06 TaskSetManager: INFO: Starting task 9.0 in stage 3.0 (TID 45, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 9, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 1.0 in stage 3.0 (TID 37) in 2145 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (2/12) 2019-10-07 18:12:06 root: INFO: at result 7, AssociativeCombiner contains 0 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Starting task 10.0 in stage 3.0 (TID 46, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 10, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 5.0 in stage 3.0 (TID 41) in 2146 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (3/12) 2019-10-07 18:12:06 root: INFO: at result 1, AssociativeCombiner contains 1 queued results 2019-10-07 18:12:06 root: INFO: at result 5, AssociativeCombiner contains 2 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Starting task 11.0 in stage 3.0 (TID 47, mw-w-0.c.broad-mpg-gnomad.internal, executor 1, partition 11, NODE_LOCAL, 7673 bytes) 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 3.0 in stage 3.0 (TID 39) in 2196 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (4/12) 2019-10-07 18:12:06 root: INFO: at result 3, AssociativeCombiner contains 3 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 2.0 in stage 3.0 (TID 38) in 2243 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (5/12) 2019-10-07 18:12:06 root: INFO: at result 2, AssociativeCombiner contains 4 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 0.0 in stage 3.0 (TID 36) in 2298 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (6/12) 2019-10-07 18:12:06 root: INFO: at result 0, AssociativeCombiner contains 3 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 4.0 in stage 3.0 (TID 40) in 2302 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (7/12) 2019-10-07 18:12:06 root: INFO: at result 4, AssociativeCombiner contains 3 queued results 2019-10-07 18:12:06 TaskSetManager: INFO: Finished task 6.0 in stage 3.0 (TID 42) in 2326 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 2) (8/12) 2019-10-07 18:12:06 root: INFO: at result 6, AssociativeCombiner contains 2 queued results 2019-10-07 18:12:09 TaskSetManager: INFO: Finished task 10.0 in stage 3.0 (TID 46) in 2952 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (9/12) 2019-10-07 18:12:09 root: INFO: at result 10, AssociativeCombiner contains 1 queued results 2019-10-07 18:12:09 TaskSetManager: INFO: Finished task 8.0 in stage 3.0 (TID 44) in 2958 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (10/12) 2019-10-07 18:12:09 root: INFO: at result 8, AssociativeCombiner contains 2 queued results 2019-10-07 18:12:09 TaskSetManager: INFO: Finished task 9.0 in stage 3.0 (TID 45) in 2968 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (11/12) 2019-10-07 18:12:09 root: INFO: at result 9, AssociativeCombiner contains 2 queued results 2019-10-07 18:12:09 TaskSetManager: INFO: Finished task 11.0 in stage 3.0 (TID 47) in 2935 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 1) (12/12) 2019-10-07 18:12:09 YarnScheduler: INFO: Removed TaskSet 3.0, whose tasks have all completed, from pool default 2019-10-07 18:12:09 DAGScheduler: INFO: ResultStage 3 (runJob at RVD.scala:611) finished in 5.145 s 2019-10-07 18:12:09 root: INFO: at result 11, AssociativeCombiner contains 1 queued results 2019-10-07 18:12:09 DAGScheduler: INFO: Job 2 finished: runJob at RVD.scala:611, took 42.896121 s 2019-10-07 18:12:09 root: INFO: optimize (Compile): before: IR size 3: (MakeTuple (0) (GetField __iruid_1728 (Ref __iruid_1727))) 2019-10-07 18:12:09 root: INFO: optimize (Compile): after: IR size 3: (MakeTuple (0) (GetField __iruid_1728 (Ref __iruid_1727))) 2019-10-07 18:12:09 MemoryStore: INFO: Block broadcast_33 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-07 18:12:09 MemoryStore: INFO: Block broadcast_33_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-07 18:12:09 BlockManagerInfo: INFO: Added broadcast_33_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 45.0 B, free: 21.7 GB) 2019-10-07 18:12:09 SparkContext: INFO: Created broadcast 33 from broadcast at SparkBackend.scala:21 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C35. instruction count: 3 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C35.apply instruction count: 76 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C35.apply instruction count: 28 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C35.setPartitionIndex instruction count: 14 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C35.addPartitionRegion instruction count: 6 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- first pass: 286.196ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 95.693ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 1m13.9s 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- compile: 9.936ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- runtime: 2.271ms 2019-10-07 18:12:09 Hail: INFO: get_gene_intervals found 5 entries: gene: GBA (ENSG00000177628) gene: IDUA (ENSG00000127415) gene: SMPD1 (ENSG00000166311) gene: GAA (ENSG00000171298) gene: GLA (ENSG00000102393) 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 1: (Literal Array[Interval[Locus(GRCh37)]] ) 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 1: (Literal Array[Interval[Locus(GRCh37)]] ) 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 1: (Literal Array[Interval[Locus(GRCh37)]] ) 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 1: (Literal Array[Interval[Locus(GRCh37)]] ) 2019-10-07 18:12:09 root: INFO: optimize (Compile): before: IR size 2: (MakeTuple (0) (Literal Array[Interval[Locus(GRCh37)]] )) 2019-10-07 18:12:09 root: INFO: optimize (Compile): after: IR size 2: (MakeTuple (0) (Literal Array[Interval[Locus(GRCh37)]] )) 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37. instruction count: 3 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.apply instruction count: 7 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.apply instruction count: 11 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_o_tuple_of_o_array_of_o_interval_of_o_locusEND_TO_o_struct_of_o_array_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_1 instruction count: 25 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_o_array_of_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_array_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_2 instruction count: 76 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_3 instruction count: 69 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_o_tuple_of_r_binaryANDr_int32END_TO_o_struct_of_r_binaryANDr_int32END_4 instruction count: 37 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_r_binary_TO_r_binary_5 instruction count: 16 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_r_int32_TO_r_int32_6 instruction count: 6 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C_etypeEncode_37.ENCODE_r_bool_TO_r_bool_7 instruction count: 6 2019-10-07 18:12:09 MemoryStore: INFO: Block broadcast_34 stored as values in memory (estimated size 184.0 B, free 21.7 GB) 2019-10-07 18:12:09 MemoryStore: INFO: Block broadcast_34_piece0 stored as bytes in memory (estimated size 143.0 B, free 21.7 GB) 2019-10-07 18:12:09 BlockManagerInfo: INFO: Added broadcast_34_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 143.0 B, free: 21.7 GB) 2019-10-07 18:12:09 SparkContext: INFO: Created broadcast 34 from broadcast at SparkBackend.scala:21 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36. instruction count: 3 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.apply instruction count: 54 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.apply instruction count: 28 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.setPartitionIndex instruction count: 14 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.addPartitionRegion instruction count: 6 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.DECODE_o_struct_of_o_array_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolENDEND_TO_o_tuple_of_o_array_of_o_interval_of_o_locusEND_3 instruction count: 46 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_o_array_of_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_array_of_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_4 instruction count: 99 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_struct_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_TO_o_tuple_of_o_tuple_of_r_binaryANDr_int32ENDANDo_tuple_of_r_binaryANDr_int32ENDANDr_boolANDr_boolEND_5 instruction count: 79 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_6 instruction count: 22 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_r_binary_TO_r_binary_7 instruction count: 29 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_r_int32_TO_r_int32_8 instruction count: 8 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.INPLACE_DECODE_r_bool_TO_r_bool_9 instruction count: 8 2019-10-07 18:12:09 root: INFO: is/hail/codegen/generated/C36.addLiterals instruction count: 30 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- first pass: 0.389ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 0.207ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 0.528ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- compile: 13.973ms 2019-10-07 18:12:09 root: INFO: Time taken for CompileAndEvaluate -- runtime: 1.869ms 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 177: (TableCount (MatrixRowsTable (MatrixFilterIntervals "[{\"start\":{\"locus\":{\"contig\":\"1\",\"position\":155204243}},\"end\":{\"locus\":{\"contig\":\"1\",\"position\":155214490}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"4\",\"position\":980785}},\"end\":{\"locus\":{\"contig\":\"4\",\"position\":998316}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"11\",\"position\":6411655}},\"end\":{\"locus\":{\"contig\":\"11\",\"position\":6416228}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"17\",\"position\":78075355}},\"end\":{\"locus\":{\"contig\":\"17\",\"position\":78093678}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"X\",\"position\":100652791}},\"end\":{\"locus\":{\"contig\":\"X\",\"position\":100662913}},\"includeStart\":true,\"includeEnd\":true}]" True (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_4" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_3" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt\",\"_spec\":null}") (Coalesce (GetField adj (Ref g)) (False))) (SelectFields (GT PID) (SelectFields (GT PID adj) (Ref g)))) (TableMapRows (TableKeyBy (s) False (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/exomes/gnomad.exomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields (s age sex hard_filters perm_filters pop_platform_filters related data_type product product_simplified qc_platform project_id project_description internal investigator known_pop known_subpop pop subpop neuro control topmed high_quality release diabetes exac_joint tcga) (SelectFields (s callrate cloudable control project_id sample_name_in_exac normalized_y_coverage gvcf internal tcga diabetes investigator mean_chr20_coverage project_description releasable_2_1 sample_name_from_bam exac_joint normalized_x_coverage pct_bases_20x pct_chimeras bam_modification neuro product age freemix product_simplified bam non_releasable esp tcga_below_30 tcga_tumor tcga_weird_barcode specific_exclusion syndip releasable_2_0_2 release_2_0_2 f_stat is_female ambiguous_sex sex_aneuploidy hard_filters perm_filters sex data_type callrate_pc1 callrate_pc2 callrate_pc3 callrate_pc4 callrate_pc5 callrate_pc6 callrate_pc7 callrate_pc8 callrate_pc9 callrate_pc10 qc_platform pop related known_pop batch qc_pop sample_qc fail_n_snp fail_r_ti_tv fail_r_insertion_deletion fail_n_insertion fail_n_deletion fail_r_het_hom_var pop_platform_filters PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 subpop known_subpop high_quality release rf_pop rf_subpop topmed) (Ref row))) None))) (InsertFields (SelectFields (s) (Ref sa)) None (meta (GetField __uid_3 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/exomes/gnomad.exomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_5 (GetField __uid_4 (Ref va)) (InsertFields (SelectFields (locus alleles) (SelectFields (locus alleles rsid qual filters info a_index was_split) (Ref va))) None (freq (GetField freq (Ref __uid_5))) (age_hist_het (GetField age_hist_het (Ref __uid_5))) (age_hist_hom (GetField age_hist_hom (Ref __uid_5))) (popmax (GetField popmax (Ref __uid_5))) (faf (GetField faf (Ref __uid_5))) (lcr (GetField lcr (Ref __uid_5))) (decoy (GetField decoy (Ref __uid_5))) (segdup (GetField segdup (Ref __uid_5))) (nonpar (GetField nonpar (Ref __uid_5))) (variant_type (GetField variant_type (Ref __uid_5))) (allele_type (GetField allele_type (Ref __uid_5))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_5))) (was_mixed (GetField was_mixed (Ref __uid_5))) (has_star (GetField has_star (Ref __uid_5))) (qd (GetField qd (Ref __uid_5))) (pab_max (GetField pab_max (Ref __uid_5))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_5))) (info_SOR (GetField info_SOR (Ref __uid_5))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_5))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_5))) (info_FS (GetField info_FS (Ref __uid_5))) (info_QD (GetField info_QD (Ref __uid_5))) (info_MQ (GetField info_MQ (Ref __uid_5))) (info_DP (GetField info_DP (Ref __uid_5))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_5))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_5))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_5))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_5))) (omni (GetField omni (Ref __uid_5))) (mills (GetField mills (Ref __uid_5))) (n_nonref (GetField n_nonref (Ref __uid_5))) (tp (GetField tp (Ref __uid_5))) (rf_train (GetField rf_train (Ref __uid_5))) (rf_label (GetField rf_label (Ref __uid_5))) (rf_probability (GetField rf_probability (Ref __uid_5))) (singleton (GetField singleton (Ref __uid_5))) (was_split (GetField was_split (Ref __uid_5))) (score (GetField score (Ref __uid_5))) (rank (GetField rank (Ref __uid_5))) (singleton_rank (GetField singleton_rank (Ref __uid_5))) (biallelic_rank (GetField biallelic_rank (Ref __uid_5))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_5))) (adj_rank (GetField adj_rank (Ref __uid_5))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_5))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_5))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_5))) (filters (GetField filters (Ref __uid_5))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_5))) (gq_hist_all (GetField gq_hist_all (Ref __uid_5))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_5))) (dp_hist_all (GetField dp_hist_all (Ref __uid_5))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_5))) (qual (GetField qual (Ref __uid_5))) (vep (GetField vep (Ref __uid_5))) (allele_info (GetField allele_info (Ref __uid_5))) (rsid (GetField rsid (Ref __uid_5)))))) (Let __uid_6 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/exomes/gnomad.exomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_6))) (freq_meta (GetField freq_meta (Ref __uid_6))) (freq_index_dict (GetField freq_index_dict (Ref __uid_6))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_6))) (age_index_dict (GetField age_index_dict (Ref __uid_6))) (faf_index_dict (GetField faf_index_dict (Ref __uid_6))) (age_distribution (GetField age_distribution (Ref __uid_6))))))))) 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'freq' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'age_hist_het' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'age_hist_hom' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'popmax' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'faf' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'lcr' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'decoy' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'segdup' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'nonpar' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'variant_type' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'allele_type' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'n_alt_alleles' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'was_mixed' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'has_star' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'qd' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'pab_max' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_MQRankSum' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_SOR' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_InbreedingCoeff' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_ReadPosRankSum' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_FS' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_QD' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_MQ' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_DP' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'transmitted_singleton' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'fail_hard_filters' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'omni' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'mills' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'n_nonref' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'tp' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rf_train' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rf_label' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rf_probability' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'singleton' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'was_split' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'score' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'singleton_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'biallelic_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_singleton_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'adj_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'adj_singleton_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'biallelic_singleton_rank' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'filters' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_alt' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_all' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_alt' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_all' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'ab_hist_alt' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'qual' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'vep' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'allele_info' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rsid' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'rf' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'freq_meta' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'freq_index_dict' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'popmax_index_dict' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'age_index_dict' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'faf_index_dict' 2019-10-07 18:12:09 root: INFO: Prune: InsertFields: eliminating field 'age_distribution' 2019-10-07 18:12:09 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 26: (TableCount (MatrixRowsTable (MatrixFilterIntervals "[{\"start\":{\"locus\":{\"contig\":\"1\",\"position\":155204243}},\"end\":{\"locus\":{\"contig\":\"1\",\"position\":155214490}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"4\",\"position\":980785}},\"end\":{\"locus\":{\"contig\":\"4\",\"position\":998316}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"11\",\"position\":6411655}},\"end\":{\"locus\":{\"contig\":\"11\",\"position\":6416228}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"17\",\"position\":78075355}},\"end\":{\"locus\":{\"contig\":\"17\",\"position\":78093678}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"X\",\"position\":100652791}},\"end\":{\"locus\":{\"contig\":\"X\",\"position\":100662913}},\"includeStart\":true,\"includeEnd\":true}]" True (MatrixFilterCols (MatrixMapCols () (MatrixAnnotateColsTable "__uid_3" (MatrixMapEntries (MatrixFilterEntries (MatrixRead Matrix{global:Struct{},col_key:[s],col:Struct{s:String},row_key:[[locus,alleles]],row:Struct{locus:Locus(GRCh37),alleles:Array[String]},entry:Struct{adj:Boolean}} False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt\",\"_spec\":null}") (Coalesce (GetField adj (Ref g)) (False))) (SelectFields () (Ref g))) (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/exomes/gnomad.exomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_3 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False)))))) 2019-10-07 18:12:11 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 153: (TableCount (TableMapRows (TableMapGlobals (TableFilterIntervals "[{\"start\":{\"locus\":{\"contig\":\"1\",\"position\":155204243}},\"end\":{\"locus\":{\"contig\":\"1\",\"position\":155214490}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"4\",\"position\":980785}},\"end\":{\"locus\":{\"contig\":\"4\",\"position\":998316}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"11\",\"position\":6411655}},\"end\":{\"locus\":{\"contig\":\"11\",\"position\":6416228}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"17\",\"position\":78075355}},\"end\":{\"locus\":{\"contig\":\"17\",\"position\":78093678}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"X\",\"position\":100652791}},\"end\":{\"locus\":{\"contig\":\"X\",\"position\":100662913}},\"includeStart\":true,\"includeEnd\":true}]" True (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapGlobals (TableMapGlobals (TableMapRows (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{adj:Boolean}]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-a23032101373\",\"references_rel_path\":\"../references\",\"table_type\":\"Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{AC:Array[Int32],AF:Array[Float64],AN:Int32,BaseQRankSum:Float64,ClippingRankSum:Float64,DB:Boolean,DP:Int32,DS:Boolean,END:Int32,FS:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,ReadPosRankSum:Float64,SOR:Float64,VQSLOD:Float64,culprit:String},a_index:Int32,was_split:Boolean}}\",\"components\":{\"globals\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"../globals/rows\"},\"rows\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"rows\"},\"partition_counts\":{\"name\":\"PartitionCountsComponentSpec\",\"counts\":[3009,2235,2256,2205,2569,2301,2260,2493,2353,2255,2395,2352,2281,2229,2215,2147,2184,2354,2610,2386,2350,2255,2205,2585,2472,2143,2226,2597,2157,2265,2611,2401,2184,2228,2269,2215,2436,2253,2319,2208,2073,2177,2192,2231,2141,2274,2168,2361,2032,2191,2253,2297,2281,2275,2325,2172,2252,2280,2222,2020,2208,2166,2241,2138,2249,2405,2259,2254,2337,2257,2200,2376,2347,2222,2191,2269,2164,2097,2201,2229,2232,2220,2156,2504,2326,2221,2272,2336,2258,2228,2206,2193,2266,2282,2519,2236,2725,2929,2414,2093,2347,2737,2358,2247,2205,2019,2135,2195,2117,2153,2331,2333,2259,2133,2274,2282,2599,2403,2593,2300,2467,2256,2212,2242,2314,2243,2216,2094,2136,2268,2284,2186,2237,2315,2348,2136,2243,2255,2222,2342,2296,2252,2198,2288,2603,2412,2368,2296,2252,2298,2423,2279,2068,2223,2347,2439,2309,2346,2403,2412,2257,2224,2532,2244,2190,2167,2137,2367,2294,2408,2274,2144,2234,2172,2171,2223,2365,2264,2378,2386,2016,2167,2389,2343,2044,2216,2065,2349,2225,2226,2269,2136,2258,2253,2142,2228,2118,2139,2195,2125,2210,2313,2263,2221,2226,2253,2224,2212,2109,2183,2268,2364,2290,2233,2249,2017,2188,2226,2286,2058,2276,2192,2140,2377,2328,2302,2239,2754,2228,2089,2156,2283,2269,2291,2364,2369,2198,2217,2053,2223,2316,2062,2186,2300,2129,2156,2364,2222,2330,2233,2205,2271,2037,2379,2201,2239,2333,2440,2116,2135,2218,1844,2209,2252,2226,2096,2353,2409,2151,2332,2278,2134,2373,2242,2338,2085,2187,2182,2233,2379,2469,2175,2505,2234,2213,2335,2355,2288,2342,2326,2179,2422,2279,2263,2171,2207,2289,2391,2109,2433,2443,2326,2286,2368,2319,2271,2243,2224,2221,2217,2519,2476,2089,2423,2327,2296,2254,2196,2274,2464,2254,2395,2151,2362,2299,2206,2083,2227,2272,2421,2142,2078,2524,2258,2230,2274,2224,2144,2226,2343,2301,2115,2233,2139,2346,2184,2313,2127,2116,2295,2579,2170,2178,2191,2226,2111,2218,2257,2191,2177,2227,2156,2238,2426,2225,2242,2225,2252,2249,2249,2205,2256,2434,2200,2406,2159,2125,2248,2257,2231,2269,2401,2195,2069,2358,2200,2010,2160,2224,2088,2173,2202,2037,2279,2304,2128,2239,2185,2140,2172,2250,2165,2096,2169,2206,2044,2224,2146,2208,2218,2196,2133,2191,2202,2009,2512,2458,2076,2428,2207,2311,2166,2224,2038,2311,2581,2431,2252,2273,2191,2375,2228,2021,2302,2177,2194,2106,2241,2183,2224,2237,2401,2438,2278,2184,2464,2282,2034,2205,2224,2084,2169,2260,2254,2191,2282,2237,2341,2390,2473,2214,2185,2184,2165,2198,2148,2214,2266,2172,2255,2264,2286,2093,2181,2337,2069,2176,2151,2111,2329,2249,2206,2282,2436,2031,2224,2430,2233,2207,2321,2202,2210,2244,2184,2108,2185,2311,2283,2475,2474,2417,2453,2529,3250,2586,2532,2605,2411,2822,2557,2632,3554,2808,2190,2279,2273,2205,2212,2401,3602,2190,2185,2049,2310,2807,3269,3404,2836,2189,2268,2218,2200,2367,2185,2209,2385,2276,2213,2208,2284,2183,2238,2236,2284,2204,2208,2368,2225,2199,2217,2342,2217,2316,2026,2001,2003,2359,2835,2284,2399,2322,2448,2248,2131,2313,2264,2162,2272,2039,2225,2175,2262,2170,2293,2134,2191,2302,2211,2323,2207,2328,2293,2145,2495,2394,2030,2275,2296,2292,2079,2234,2313,2301,2272,2388,2312,2230,2206,2238,2128,2411,2274,2343,2289,2188,2290,2245,2364,2324,2260,2092,2258,2237,2240,2233,2224,2161,1938,2243,2219,2268,2265,2263,2251,2152,2036,2263,2317,2257,2170,2351,2269,2208,2338,2658,2536,2012,2162,2220,2441,2169,2350,2250,2327,2322,2406,2240,2538,2217,2448,2266,2195,2254,2205,2295,2277,2405,2115,2399,2354,2193,2328,2277,2141,2253,2205,2481,2066,2287,2238,2518,2278,2194,2213,2207,2444,2396,2331,2297,2245,2126,2425,2178,2129,2153,2255,2250,2500,2265,1990,2190,2277,2183,2180,2197,2269,2237,2345,2121,2331,2226,2196,2276,2265,2240,2111,2181,2239,2252,2216,2169,2174,2098,2230,2168,2017,2287,2258,2188,2271,2141,2312,2502,2357,2208,2169,2292,2335,2287,2249,2254,2043,2187,2186,2225,2386,2406,2353,2004,2197,2141,2208,2354,2255,2070,2240,2243,2167,2239,2211,2070,2304,2302,2330,2343,2277,2322,2167,2191,2148,2227,2219,2402,2475,2657,243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(InsertFields (Ref global) None (__cols (GetField rows (TableCollect (TableRead Table{global:Struct{},key:[],row:Struct{s:String}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-a23032101373\",\"references_rel_path\":\"../references\",\"table_type\":\"Table{global:Struct{},key:[s],row:Struct{s:String}}\",\"components\":{\"globals\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"../globals/rows\"},\"rows\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"rows\"},\"partition_counts\":{\"name\":\"PartitionCountsComponentSpec\",\"counts\":[164332]}}}}")))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap i (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let g (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i)) (If (Let sa (ArrayRef (GetField __cols (Ref global)) (Ref i)) (ApplyUnaryPrimOp Bang (Coalesce (GetField adj (Ref g)) (False)))) (NA Struct{adj:Boolean}) (Ref g))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap i (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let g (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i)) (Let sa (ArrayRef (GetField __cols (Ref global)) (Ref i)) (SelectFields () (Ref g)))))))) (Let __dictfield (ToDict (ArrayMap __iruid_2107 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/exomes/gnomad.exomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_2107)) (SelectFields (release) (Ref __iruid_2107))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_2106 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_2106) None (__uid_3 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_2106)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_2111 (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let __cols_array (GetField __cols (Ref global)) (Let sa (ArrayRef (Ref __cols_array) (Ref __iruid_2111)) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_3 (Ref sa)))))))))) (InsertFields (Ref global) None (newColIdx (ArrayFilter i (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let sa (ArrayRef (GetField __cols (Ref global)) (Ref i)) (Coalesce (GetField release (GetField meta (Ref sa))) (False))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap i (GetField newColIdx (Ref global)) (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i)))))) (SelectFields (__cols) (InsertFields (Ref global) None (__cols (ArrayMap i (GetField newColIdx (Ref global)) (ArrayRef (GetField __cols (Ref global)) (Ref i)))))))) (SelectFields () (Ref global))) (SelectFields (locus alleles) (Ref row)))) 2019-10-07 18:12:11 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 3: (TableCount (TableFilterIntervals "[{\"start\":{\"locus\":{\"contig\":\"1\",\"position\":155204243}},\"end\":{\"locus\":{\"contig\":\"1\",\"position\":155214490}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"4\",\"position\":980785}},\"end\":{\"locus\":{\"contig\":\"4\",\"position\":998316}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"11\",\"position\":6411655}},\"end\":{\"locus\":{\"contig\":\"11\",\"position\":6416228}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"17\",\"position\":78075355}},\"end\":{\"locus\":{\"contig\":\"17\",\"position\":78093678}},\"includeStart\":true,\"includeEnd\":true},{\"start\":{\"locus\":{\"contig\":\"X\",\"position\":100652791}},\"end\":{\"locus\":{\"contig\":\"X\",\"position\":100662913}},\"includeStart\":true,\"includeEnd\":true}]" True (TableRead Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-a23032101373\",\"references_rel_path\":\"../references\",\"table_type\":\"Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{AC:Array[Int32],AF:Array[Float64],AN:Int32,BaseQRankSum:Float64,ClippingRankSum:Float64,DB:Boolean,DP:Int32,DS:Boolean,END:Int32,FS:Float64,HaplotypeScore:Float64,InbreedingCoeff:Float64,MLEAC:Array[Int32],MLEAF:Array[Float64],MQ:Float64,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,ReadPosRankSum:Float64,SOR:Float64,VQSLOD:Float64,culprit:String},a_index:Int32,was_split:Boolean}}\",\"components\":{\"globals\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"../globals/rows\"},\"rows\":{\"name\":\"RVDComponentSpec\",\"rel_path\":\"rows\"},\"partition_counts\":{\"name\":\"PartitionCountsComponentSpec\",\"counts\":[3009,2235,2256,2205,2569,2301,2260,2493,2353,2255,2395,2352,2281,2229,2215,2147,2184,2354,2610,2386,2350,2255,2205,2585,2472,2143,2226,2597,2157,2265,2611,2401,2184,2228,2269,2215,2436,2253,2319,2208,2073,2177,2192,2231,2141,2274,2168,2361,2032,2191,2253,2297,2281,2275,2325,2172,2252,2280,2222,2020,2208,2166,2241,2138,2249,2405,2259,2254,2337,2257,2200,2376,2347,2222,2191,2269,2164,2097,2201,2229,2232,2220,2156,2504,2326,2221,2272,2336,2258,2228,2206,2193,2266,2282,2519,2236,2725,2929,2414,2093,2347,2737,2358,2247,2205,2019,2135,2195,2117,2153,2331,2333,2259,2133,2274,2282,2599,2403,2593,2300,2467,2256,2212,2242,2314,2243,2216,2094,2136,2268,2284,2186,2237,2315,2348,2136,2243,2255,2222,2342,2296,2252,2198,2288,2603,2412,2368,2296,2252,2298,2423,2279,2068,2223,2347,2439,2309,2346,2403,2412,2257,2224,2532,2244,2190,2167,2137,2367,2294,2408,2274,2144,2234,2172,2171,2223,2365,2264,2378,2386,2016,2167,2389,2343,2044,2216,2065,2349,2225,2226,2269,2136,2258,2253,2142,2228,2118,2139,2195,2125,2210,2313,2263,2221,2226,2253,2224,2212,2109,2183,2268,2364,2290,2233,2249,2017,2188,2226,2286,2058,2276,2192,2140,2377,2328,2302,2239,2754,2228,2089,2156,2283,2269,2291,2364,2369,2198,2217,2053,2223,2316,2062,2186,2300,2129,2156,2364,2222,2330,2233,2205,2271,2037,2379,2201,2239,2333,2440,2116,2135,2218,1844,2209,2252,2226,2096,2353,2409,2151,2332,2278,2134,2373,2242,2338,2085,2187,2182,2233,2379,2469,2175,2505,2234,2213,2335,2355,2288,2342,2326,2179,2422,2279,2263,2171,2207,2289,2391,2109,2433,2443,2326,2286,2368,2319,2271,2243,2224,2221,2217,2519,2476,2089,2423,2327,2296,2254,2196,2274,2464,2254,2395,2151,2362,2299,2206,2083,2227,2272,2421,2142,2078,2524,2258,2230,2274,2224,2144,2226,2343,2301,2115,2233,2139,2346,2184,2313,2127,2116,2295,2579,2170,2178,2191,2226,2111,2218,2257,2191,2177,2227,2156,2238,2426,2225,2242,2225,2252,2249,2249,2205,2256,2434,2200,2406,2159,2125,2248,2257,2231,2269,2401,2195,2069,2358,2200,2010,2160,2224,2088,2173,2202,2037,2279,2304,2128,2239,2185,2140,2172,2250,2165,2096,2169,2206,2044,2224,2146,2208,2218,2196,2133,2191,2202,2009,2512,2458,2076,2428,2207,2311,2166,2224,2038,2311,2581,2431,2252,2273,2191,2375,2228,2021,2302,2177,2194,2106,2241,2183,2224,2237,2401,2438,2278,2184,2464,2282,2034,2205,2224,2084,2169,2260,2254,2191,2282,2237,2341,2390,2473,2214,2185,2184,2165,2198,2148,2214,2266,2172,2255,2264,2286,2093,2181,2337,2069,2176,2151,2111,2329,2249,2206,2282,2436,2031,2224,2430,2233,2207,2321,2202,2210,2244,2184,2108,2185,2311,2283,2475,2474,2417,2453,2529,3250,2586,2532,2605,2411,2822,2557,2632,3554,2808,2190,2279,2273,2205,2212,2401,3602,2190,2185,2049,2310,2807,3269,3404,2836,2189,2268,2218,2200,2367,2185,2209,2385,2276,2213,2208,2284,2183,2238,2236,2284,2204,2208,2368,2225,2199,2217,2342,2217,2316,2026,2001,2003,2359,2835,2284,2399,2322,2448,2248,2131,2313,2264,2162,2272,2039,2225,2175,2262,2170,2293,2134,2191,2302,2211,2323,2207,2328,2293,2145,2495,2394,2030,2275,2296,2292,2079,2234,2313,2301,2272,2388,2312,2230,2206,2238,2128,2411,2274,2343,2289,2188,2290,2245,2364,2324,2260,2092,2258,2237,2240,2233,2224,2161,1938,2243,2219,2268,2265,2263,2251,2152,2036,2263,2317,2257,2170,2351,2269,2208,2338,2658,2536,2012,2162,2220,2441,2169,2350,2250,2327,2322,2406,2240,2538,2217,2448,2266,2195,2254,2205,2295,2277,2405,2115,2399,2354,2193,2328,2277,2141,2253,2205,2481,2066,2287,2238,2518,2278,2194,2213,2207,2444,2396,2331,2297,2245,2126,2425,2178,2129,2153,2255,2250,2500,2265,1990,2190,2277,2183,2180,2197,2269,2237,2345,2121,2331,2226,2196,2276,2265,2240,2111,2181,2239,2252,2216,2169,2174,2098,2230,2168,2017,2287,2258,2188,2271,2141,2312,2502,2357,2208,2169,2292,2335,2287,2249,2254,2043,2187,2186,2225,2386,2406,2353,2004,2197,2141,2208,2354,2255,2070,2240,2243,2167,2239,2211,2070,2304,2302,2330,2343,2277,2322,2167,2191,2148,2227,2219,2402,2475,2657,243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2019-10-07 18:12:11 root: INFO: is/hail/codegen/generated/C_etypeDecode_38. instruction count: 3 2019-10-07 18:12:11 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.apply instruction count: 7 2019-10-07 18:12:11 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.apply instruction count: 12 2019-10-07 18:12:11 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39. instruction count: 3 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.apply instruction count: 7 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.apply instruction count: 12 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.DECODE_o_struct_of_o_struct_of_r_binaryANDr_int32ENDANDo_array_of_o_binaryANDo_binaryANDo_float64ANDo_array_of_o_binaryANDo_struct_of_o_array_of_o_int32ANDo_array_of_o_float64ANDo_int32ANDo_float64ANDo_float64ANDo_boolANDo_int32ANDo_boolANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_int32ANDo_boolEND_TO_o_tuple_of_o_locusANDo_array_of_o_stringEND_1 instruction count: 155 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_2 instruction count: 22 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_r_binary_TO_r_binary_3 instruction count: 29 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_r_int32_TO_r_int32_4 instruction count: 8 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_array_of_o_binary_TO_o_array_of_o_binary_5 instruction count: 99 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_binary_TO_o_binary_6 instruction count: 29 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_binary_7 instruction count: 9 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_float64_8 instruction count: 5 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_array_of_o_binary_9 instruction count: 54 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_struct_of_o_array_of_o_int32ANDo_array_of_o_float64ANDo_int32ANDo_float64ANDo_float64ANDo_boolANDo_int32ANDo_boolANDo_int32ANDo_float64ANDo_float64ANDo_float64ANDo_array_of_o_int32ANDo_array_of_o_float64ANDo_float64ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryEND_10 instruction count: 351 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_array_of_o_int32_11 instruction count: 54 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_int32_12 instruction count: 5 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_array_of_o_float64_13 instruction count: 54 2019-10-07 18:12:12 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_bool_14 instruction count: 5 2019-10-07 18:12:12 MemoryStore: INFO: Block broadcast_35 stored as values in memory (estimated size 401.3 KB, free 21.7 GB) 2019-10-07 18:12:12 MemoryStore: INFO: Block broadcast_35_piece0 stored as bytes in memory (estimated size 28.2 KB, free 21.7 GB) 2019-10-07 18:12:12 BlockManagerInfo: INFO: Added broadcast_35_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:34837 (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:12:12 SparkContext: INFO: Created broadcast 35 from broadcast at HailContext.scala:617 2019-10-07 18:12:12 root: ERROR: IllegalArgumentException: requirement failed From java.lang.IllegalArgumentException: requirement failed at scala.Predef$.require(Predef.scala:212) at is.hail.expr.ir.TableValue.(TableValue.scala:47) at is.hail.expr.ir.TableNativeZippedReader.apply(TableIR.scala:245) at is.hail.expr.ir.TableRead.execute(TableIR.scala:295) at is.hail.expr.ir.TableFilterIntervals.execute(TableIR.scala:1714) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply$mcJ$sp(Interpret.scala:730) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:730) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:730) at scala.Option.getOrElse(Option.scala:121) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:730) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:89) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:59) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$7.apply(InterpretNonCompilable.scala:19) at is.hail.expr.ir.InterpretNonCompilable$$anonfun$7.apply(InterpretNonCompilable.scala:19) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:186) at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:19) at is.hail.expr.ir.CompileAndEvaluate$$anonfun$2.apply(CompileAndEvaluate.scala:37) at is.hail.expr.ir.CompileAndEvaluate$$anonfun$2.apply(CompileAndEvaluate.scala:37) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:24) at is.hail.expr.ir.CompileAndEvaluate$.apply(CompileAndEvaluate.scala:37) at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:55) at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:55) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:8) at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:7) at is.hail.utils.package$.using(package.scala:596) at is.hail.annotations.Region$.scoped(Region.scala:18) at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:7) at is.hail.backend.Backend.execute(Backend.scala:55) at is.hail.backend.Backend.executeJSON(Backend.scala:61) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.lang.Thread.run(Thread.java:748) 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 33 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 90 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 28 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 57 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 81 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 80 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 31 2019-10-07 18:12:12 ContextCleaner: INFO: Cleaned accumulator 38 2019-10-07 18:12:12 SparkContext: INFO: Invoking stop() from shutdown hook 2019-10-07 18:12:12 BlockManagerInfo: INFO: Removed broadcast_31_piece0 on mw-m.c.broad-mpg-gnomad.internal:34837 in memory (size: 41.6 KB, free: 21.7 GB) 2019-10-07 18:12:12 BlockManagerInfo: INFO: Removed broadcast_31_piece0 on mw-w-0.c.broad-mpg-gnomad.internal:37157 in memory (size: 41.6 KB, free: 9.5 GB) 2019-10-07 18:12:12 BlockManagerInfo: INFO: Removed broadcast_31_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:39849 in memory (size: 41.6 KB, free: 9.5 GB) 2019-10-07 18:12:12 AbstractConnector: INFO: Stopped Spark@ee7ac84{HTTP/1.1,[http/1.1]}{0.0.0.0:4041} 2019-10-07 18:12:13 SparkUI: INFO: Stopped Spark web UI at http://mw-m.c.broad-mpg-gnomad.internal:4041 2019-10-07 18:12:13 ContextCleaner: INFO: Cleaned accumulator 49 2019-10-07 18:12:13 ContextCleaner: INFO: Cleaned accumulator 84 2019-10-07 18:12:13 BlockManagerInfo: INFO: Removed broadcast_12_piece0 on mw-m.c.broad-mpg-gnomad.internal:34837 in memory (size: 28.2 KB, free: 21.7 GB) 2019-10-07 18:12:13 BlockManagerInfo: INFO: Removed broadcast_12_piece0 on mw-w-0.c.broad-mpg-gnomad.internal:37157 in memory (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:12:13 BlockManagerInfo: INFO: Removed broadcast_12_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:39849 in memory (size: 28.2 KB, free: 9.5 GB) 2019-10-07 18:12:13 YarnClientSchedulerBackend: INFO: Interrupting monitor thread 2019-10-07 18:12:13 YarnClientSchedulerBackend: INFO: Shutting down all executors 2019-10-07 18:12:13 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Asking each executor to shut down 2019-10-07 18:12:13 SchedulerExtensionServices: INFO: Stopping SchedulerExtensionServices (serviceOption=None, services=List(), started=false) 2019-10-07 18:12:13 YarnClientSchedulerBackend: INFO: Stopped 2019-10-07 18:12:13 MapOutputTrackerMasterEndpoint: INFO: MapOutputTrackerMasterEndpoint stopped! 2019-10-07 18:12:13 MemoryStore: INFO: MemoryStore cleared 2019-10-07 18:12:13 BlockManager: INFO: BlockManager stopped 2019-10-07 18:12:13 BlockManagerMaster: INFO: BlockManagerMaster stopped 2019-10-07 18:12:13 OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: INFO: OutputCommitCoordinator stopped! 2019-10-07 18:12:13 SparkContext: INFO: Successfully stopped SparkContext 2019-10-07 18:12:13 ShutdownHookManager: INFO: Shutdown hook called 2019-10-07 18:12:13 ShutdownHookManager: INFO: Deleting directory /hadoop/spark/tmp/spark-115a38c9-ae53-401a-9f19-b51ab63a1e36/pyspark-a9b59884-1807-42b4-b163-d5bb0d5e4ade 2019-10-07 18:12:13 ShutdownHookManager: INFO: Deleting directory /hadoop/spark/tmp/spark-115a38c9-ae53-401a-9f19-b51ab63a1e36 2019-10-07 18:12:13 ShutdownHookManager: INFO: Deleting directory /tmp/spark-2038360b-8e49-42ee-bf02-09b08f8c2577