2019-10-08 20:47:12 Hail: WARN: This Hail JAR was compiled for Spark 2.4.0, running with Spark 2.4.4. Compatibility is not guaranteed. 2019-10-08 20:47:12 SparkContext: INFO: Running Spark version 2.4.4 2019-10-08 20:47:12 SparkContext: INFO: Submitted application: Hail 2019-10-08 20:47:12 SparkContext: INFO: Spark configuration: spark.app.name=Hail spark.driver.extraClassPath=/opt/conda/default/lib/python3.6/site-packages/hail/hail-all-spark.jar,/opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.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.extraListeners=sparkmonitor.listener.JupyterSparkMonitorListener 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,file:/opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.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,file:///opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.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.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,file:///opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.jar spark.yarn.executor.failuresValidityInterval=1h spark.yarn.historyServer.address=mw-m:18080 spark.yarn.isPython=true spark.yarn.jars=local:/usr/lib/spark/jars/* 2019-10-08 20:47:12 SecurityManager: INFO: Changing view acls to: root 2019-10-08 20:47:12 SecurityManager: INFO: Changing modify acls to: root 2019-10-08 20:47:12 SecurityManager: INFO: Changing view acls groups to: 2019-10-08 20:47:12 SecurityManager: INFO: Changing modify acls groups to: 2019-10-08 20:47:12 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() 2019-10-08 20:47:13 Utils: INFO: Successfully started service 'sparkDriver' on port 45347. 2019-10-08 20:47:13 SparkEnv: INFO: Registering MapOutputTracker 2019-10-08 20:47:13 SparkEnv: INFO: Registering BlockManagerMaster 2019-10-08 20:47:13 BlockManagerMasterEndpoint: INFO: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information 2019-10-08 20:47:13 BlockManagerMasterEndpoint: INFO: BlockManagerMasterEndpoint up 2019-10-08 20:47:13 DiskBlockManager: INFO: Created local directory at /hadoop/spark/tmp/blockmgr-8f37b5f7-1cf7-4c05-aacd-1fccf25e5092 2019-10-08 20:47:13 MemoryStore: INFO: MemoryStore started with capacity 21.7 GB 2019-10-08 20:47:13 SparkEnv: INFO: Registering OutputCommitCoordinator 2019-10-08 20:47:13 log: INFO: Logging initialized @3428ms 2019-10-08 20:47:13 Server: INFO: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown 2019-10-08 20:47:13 Server: INFO: Started @3538ms 2019-10-08 20:47:13 AbstractConnector: INFO: Started ServerConnector@a81a2f9{HTTP/1.1,[http/1.1]}{0.0.0.0:4040} 2019-10-08 20:47:13 Utils: INFO: Successfully started service 'SparkUI' on port 4040. 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@2c693f3a{/jobs,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@1e98a75{/jobs/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@b4de0d1{/jobs/job,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@118c5a3a{/jobs/job/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@75a36bb2{/stages,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@1bf2f3e{/stages/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@389d2a2{/stages/stage,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@66890409{/stages/stage/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@2bd8d6b8{/stages/pool,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@631cc2bd{/stages/pool/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@457c769e{/storage,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@6bfb9b74{/storage/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@67beda5{/storage/rdd,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@377defd{/storage/rdd/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@2519808b{/environment,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@128e9f67{/environment/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@4bc15e56{/executors,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@767cf1e5{/executors/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@1f882a79{/executors/threadDump,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@791bfb48{/executors/threadDump/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@38e939d3{/static,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@5f0a632{/,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@42c9f39b{/api,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@6bf96ba9{/jobs/job/kill,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@192c7a1a{/stages/stage/kill,null,AVAILABLE,@Spark} 2019-10-08 20:47:13 SparkUI: INFO: Bound SparkUI to 0.0.0.0, and started at http://mw-m.c.broad-mpg-gnomad.internal:4040 2019-10-08 20:47:13 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:45347/jars/hail-all-spark.jar with timestamp 1570567633649 2019-10-08 20:47:13 SparkContext: INFO: Added JAR file:/opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.jar at spark://mw-m.c.broad-mpg-gnomad.internal:45347/jars/listener.jar with timestamp 1570567633650 2019-10-08 20:47:13 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. 2019-10-08 20:47:13 FairSchedulableBuilder: INFO: Created default pool: default, schedulingMode: FIFO, minShare: 0, weight: 1 2019-10-08 20:47:13 Utils: INFO: Using initial executors = 2, max of spark.dynamicAllocation.initialExecutors, spark.dynamicAllocation.minExecutors and spark.executor.instances 2019-10-08 20:47:14 RMProxy: INFO: Connecting to ResourceManager at mw-m/10.128.0.27:8032 2019-10-08 20:47:14 AHSProxy: INFO: Connecting to Application History server at mw-m/10.128.0.27:10200 2019-10-08 20:47:14 Client: INFO: Requesting a new application from cluster with 2 NodeManagers 2019-10-08 20:47:14 Client: INFO: Verifying our application has not requested more than the maximum memory capability of the cluster (40960 MB per container) 2019-10-08 20:47:14 Client: INFO: Will allocate AM container, with 1024 MB memory including 384 MB overhead 2019-10-08 20:47:14 Client: INFO: Setting up container launch context for our AM 2019-10-08 20:47:14 Client: INFO: Setting up the launch environment for our AM container 2019-10-08 20:47:14 Client: INFO: Preparing resources for our AM container 2019-10-08 20:47:14 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_1570567361101_0001/hail-all-spark.jar 2019-10-08 20:47:15 Client: INFO: Uploading resource file:/opt/conda/default/lib/python3.6/site-packages/sparkmonitor/listener.jar -> hdfs://mw-m/user/root/.sparkStaging/application_1570567361101_0001/listener.jar 2019-10-08 20:47:15 Client: INFO: Uploading resource file:/usr/lib/spark/python/lib/pyspark.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570567361101_0001/pyspark.zip 2019-10-08 20:47:15 Client: INFO: Uploading resource file:/usr/lib/spark/python/lib/py4j-0.10.7-src.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570567361101_0001/py4j-0.10.7-src.zip 2019-10-08 20:47:16 Client: INFO: Uploading resource file:/hadoop/spark/tmp/spark-068a09f4-7e7a-48de-b23a-7641e7f0f896/__spark_conf__2209105967323977628.zip -> hdfs://mw-m/user/root/.sparkStaging/application_1570567361101_0001/__spark_conf__.zip 2019-10-08 20:47:16 SecurityManager: INFO: Changing view acls to: root 2019-10-08 20:47:16 SecurityManager: INFO: Changing modify acls to: root 2019-10-08 20:47:16 SecurityManager: INFO: Changing view acls groups to: 2019-10-08 20:47:16 SecurityManager: INFO: Changing modify acls groups to: 2019-10-08 20:47:16 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() 2019-10-08 20:47:18 Client: INFO: Submitting application application_1570567361101_0001 to ResourceManager 2019-10-08 20:47:18 YarnClientImpl: INFO: Submitted application application_1570567361101_0001 2019-10-08 20:47:18 SchedulerExtensionServices: INFO: Starting Yarn extension services with app application_1570567361101_0001 and attemptId None 2019-10-08 20:47:19 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:19 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: 1570567638279 final status: UNDEFINED tracking URL: http://mw-m:8088/proxy/application_1570567361101_0001/ user: root 2019-10-08 20:47:20 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:21 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:22 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:23 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:24 Client: INFO: Application report for application_1570567361101_0001 (state: ACCEPTED) 2019-10-08 20:47:25 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_1570567361101_0001), /proxy/application_1570567361101_0001 2019-10-08 20:47:25 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. 2019-10-08 20:47:25 YarnSchedulerBackend$YarnSchedulerEndpoint: INFO: ApplicationMaster registered as NettyRpcEndpointRef(spark-client://YarnAM) 2019-10-08 20:47:25 Client: INFO: Application report for application_1570567361101_0001 (state: RUNNING) 2019-10-08 20:47:25 Client: INFO: client token: N/A diagnostics: N/A ApplicationMaster host: 10.128.0.15 ApplicationMaster RPC port: -1 queue: default start time: 1570567638279 final status: UNDEFINED tracking URL: http://mw-m:8088/proxy/application_1570567361101_0001/ user: root 2019-10-08 20:47:25 YarnClientSchedulerBackend: INFO: Application application_1570567361101_0001 has started running. 2019-10-08 20:47:25 Utils: INFO: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43029. 2019-10-08 20:47:25 NettyBlockTransferService: INFO: Server created on mw-m.c.broad-mpg-gnomad.internal:43029 2019-10-08 20:47:25 BlockManager: INFO: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy 2019-10-08 20:47:25 BlockManagerMaster: INFO: Registering BlockManager BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 43029, None) 2019-10-08 20:47:25 BlockManagerMasterEndpoint: INFO: Registering block manager mw-m.c.broad-mpg-gnomad.internal:43029 with 21.7 GB RAM, BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 43029, None) 2019-10-08 20:47:25 BlockManagerMaster: INFO: Registered BlockManager BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 43029, None) 2019-10-08 20:47:25 BlockManager: INFO: external shuffle service port = 7337 2019-10-08 20:47:25 BlockManager: INFO: Initialized BlockManager: BlockManagerId(driver, mw-m.c.broad-mpg-gnomad.internal, 43029, None) 2019-10-08 20:47:25 JettyUtils: INFO: Adding filter org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter to /metrics/json. 2019-10-08 20:47:25 ContextHandler: INFO: Started o.s.j.s.ServletContextHandler@16aef473{/metrics/json,null,AVAILABLE,@Spark} 2019-10-08 20:47:26 EventLoggingListener: INFO: Logging events to hdfs://mw-m/user/spark/eventlog/application_1570567361101_0001 2019-10-08 20:47:26 Utils: INFO: Using initial executors = 2, max of spark.dynamicAllocation.initialExecutors, spark.dynamicAllocation.minExecutors and spark.executor.instances 2019-10-08 20:47:26 SparkContext: INFO: Registered listener sparkmonitor.listener.JupyterSparkMonitorListener 2019-10-08 20:47:26 YarnClientSchedulerBackend: INFO: SchedulerBackend is ready for scheduling beginning after reached minRegisteredResourcesRatio: 0.0 2019-10-08 20:47:26 Hail: INFO: Hail temporary directory: hdfs://mw-m/tmp/hail.YUkfyjiRMjhG 2019-10-08 20:47:26 Hail: INFO: SparkUI: http://mw-m.c.broad-mpg-gnomad.internal:4040 2019-10-08 20:47:26 Hail: INFO: Running Hail version 0.2.24-aca727e8d9c9 2019-10-08 20:47:27 SparkContext: WARN: Using an existing SparkContext; some configuration may not take effect. 2019-10-08 20:47:28 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.15:34450) with ID 1 2019-10-08 20:47:28 ExecutorAllocationManager: INFO: New executor 1 has registered (new total is 1) 2019-10-08 20:47:28 BlockManagerMasterEndpoint: INFO: Registering block manager mw-w-1.c.broad-mpg-gnomad.internal:42975 with 9.5 GB RAM, BlockManagerId(1, mw-w-1.c.broad-mpg-gnomad.internal, 42975, None) 2019-10-08 20:47:31 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Registered executor NettyRpcEndpointRef(spark-client://Executor) (10.128.0.17:40796) with ID 2 2019-10-08 20:47:31 ExecutorAllocationManager: INFO: New executor 2 has registered (new total is 2) 2019-10-08 20:47:32 BlockManagerMasterEndpoint: INFO: Registering block manager mw-w-0.c.broad-mpg-gnomad.internal:33869 with 9.5 GB RAM, BlockManagerId(2, mw-w-0.c.broad-mpg-gnomad.internal, 33869, None) 2019-10-08 20:47:41 ZlibFactory: INFO: Successfully loaded & initialized native-zlib library 2019-10-08 20:47:41 CodecPool: INFO: Got brand-new decompressor [.gz] 2019-10-08 20:47:43 MemoryStore: INFO: Block broadcast_0 stored as values in memory (estimated size 47.4 KB, free 21.7 GB) 2019-10-08 20:47:43 MemoryStore: INFO: Block broadcast_0_piece0 stored as bytes in memory (estimated size 2.9 KB, free 21.7 GB) 2019-10-08 20:47:43 BlockManagerInfo: INFO: Added broadcast_0_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 2.9 KB, free: 21.7 GB) 2019-10-08 20:47:43 SparkContext: INFO: Created broadcast 0 from broadcast at SparkBackend.scala:21 2019-10-08 20:47:45 root: INFO: RegionPool: initialized for thread 17: Thread-5 2019-10-08 20:47:45 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 185: (TableCount (MatrixRowsTable (MatrixMapGlobals (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/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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/genomes/gnomad.genomes.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))) (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))) (rank (GetField rank (Ref __uid_5))) (was_split (GetField was_split (Ref __uid_5))) (singleton (GetField singleton (Ref __uid_5))) (_score (GetField _score (Ref __uid_5))) (_singleton (GetField _singleton (Ref __uid_5))) (biallelic_rank (GetField biallelic_rank (Ref __uid_5))) (singleton_rank (GetField singleton_rank (Ref __uid_5))) (n_nonref (GetField n_nonref (Ref __uid_5))) (score (GetField score (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/genomes/gnomad.genomes.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)))))) (InsertFields (SelectFields () (SelectFields (rf freq_meta freq_index_dict popmax_index_dict age_index_dict faf_index_dict age_distribution) (Ref global))) None)))) 2019-10-08 20:47:45 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 1: (I64 290745715) 2019-10-08 20:47:45 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 1: (I64 290745715) 2019-10-08 20:47:45 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 1: (I64 290745715) 2019-10-08 20:47:46 root: INFO: optimize (Compile): before: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:47:46 root: INFO: optimize (Compile): after: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:47:46 MemoryStore: INFO: Block broadcast_1 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:47:46 MemoryStore: INFO: Block broadcast_1_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:47:46 BlockManagerInfo: INFO: Added broadcast_1_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:47:46 SparkContext: INFO: Created broadcast 1 from broadcast at SparkBackend.scala:21 2019-10-08 20:47:46 root: INFO: is/hail/codegen/generated/C0. instruction count: 3 2019-10-08 20:47:46 root: INFO: is/hail/codegen/generated/C0.apply instruction count: 53 2019-10-08 20:47:46 root: INFO: is/hail/codegen/generated/C0.apply instruction count: 28 2019-10-08 20:47:46 root: INFO: is/hail/codegen/generated/C0.setPartitionIndex instruction count: 14 2019-10-08 20:47:46 root: INFO: is/hail/codegen/generated/C0.addPartitionRegion instruction count: 6 2019-10-08 20:47:46 root: INFO: Time taken for CompileAndEvaluate -- first pass: 126.104ms 2019-10-08 20:47:46 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 0.646ms 2019-10-08 20:47:46 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 10.291ms 2019-10-08 20:47:46 root: INFO: Time taken for CompileAndEvaluate -- compile: 164.087ms 2019-10-08 20:47:46 root: INFO: Time taken for CompileAndEvaluate -- runtime: 12.371ms 2019-10-08 20:47:46 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 185: (TableCount (MatrixColsTable (MatrixMapGlobals (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/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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/genomes/gnomad.genomes.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))) (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))) (rank (GetField rank (Ref __uid_5))) (was_split (GetField was_split (Ref __uid_5))) (singleton (GetField singleton (Ref __uid_5))) (_score (GetField _score (Ref __uid_5))) (_singleton (GetField _singleton (Ref __uid_5))) (biallelic_rank (GetField biallelic_rank (Ref __uid_5))) (singleton_rank (GetField singleton_rank (Ref __uid_5))) (n_nonref (GetField n_nonref (Ref __uid_5))) (score (GetField score (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/genomes/gnomad.genomes.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)))))) (InsertFields (SelectFields () (SelectFields (rf freq_meta freq_index_dict popmax_index_dict age_index_dict faf_index_dict age_distribution) (Ref global))) None)))) 2019-10-08 20:47:46 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 25: (TableCount (MatrixColsTable (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/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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))))) 2019-10-08 20:47:47 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 155: (TableCount (TableKeyBy () False (TableParallelize None (Let __cols_and_globals (TableGetGlobals (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/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (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_36 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_36)) (SelectFields (release) (Ref __iruid_36))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_35 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_35) None (__uid_3 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_35)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_40 (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_40)) (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)))))))) (MakeStruct (rows (GetField __cols (Ref __cols_and_globals))) (global (SelectFields () (Ref __cols_and_globals)))))))) 2019-10-08 20:47:47 root: INFO: Prune: MakeStruct: eliminating field 'global' 2019-10-08 20:47:47 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 61: (Cast Int64 (ArrayLen (GetField rows (Let __iruid_154 (ToDict (ArrayMap __iruid_155 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_155)) (SelectFields (release) (Ref __iruid_155))))) (Let __iruid_156 (ArrayMap __iruid_157 (GetField rows (TableCollect (TableRead Table{global:Struct{},key:[],row:Struct{s:String}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}"))) (InsertFields (Ref __iruid_157) None (__uid_3 (ApplyIR get Struct{release:Boolean} (Ref __iruid_154) (MakeStruct (s (GetField s (Ref __iruid_157)))))))) (Let __iruid_158 (ArrayMap __iruid_159 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_156)) (I32 1)) (Let __iruid_160 (ArrayRef (Ref __iruid_156) (Ref __iruid_159)) (InsertFields (SelectFields () (Ref __iruid_160)) None (meta (GetField __uid_3 (Ref __iruid_160)))))) (MakeStruct (rows (ArrayMap __iruid_161 (ArrayFilter __iruid_162 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_158)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_158) (Ref __iruid_162)))) (False))) (ArrayRef (Ref __iruid_158) (Ref __iruid_161))))))))))) 2019-10-08 20:47:47 root: INFO: is/hail/codegen/generated/C_etypeDecode_1. instruction count: 3 2019-10-08 20:47:47 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.apply instruction count: 7 2019-10-08 20:47:47 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.apply instruction count: 12 2019-10-08 20:47:47 root: INFO: is/hail/codegen/generated/C_etypeDecode_1.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeDecode_2. instruction count: 3 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeDecode_2.apply instruction count: 7 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeDecode_2.apply instruction count: 12 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeDecode_2.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeDecode_2.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:47:48 MemoryStore: INFO: Block broadcast_2 stored as values in memory (estimated size 401.3 KB, free 21.7 GB) 2019-10-08 20:47:48 MemoryStore: INFO: Block broadcast_2_piece0 stored as bytes in memory (estimated size 28.2 KB, free 21.7 GB) 2019-10-08 20:47:48 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 28.2 KB, free: 21.7 GB) 2019-10-08 20:47:48 SparkContext: INFO: Created broadcast 2 from broadcast at HailContext.scala:617 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeEncode_3. instruction count: 3 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeEncode_3.apply instruction count: 7 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeEncode_3.apply instruction count: 11 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeEncode_3.ENCODE_o_tuple_of_o_stringEND_TO_o_struct_of_o_binaryEND_1 instruction count: 25 2019-10-08 20:47:48 root: INFO: is/hail/codegen/generated/C_etypeEncode_3.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:47:48 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:47:48 DAGScheduler: INFO: Got job 0 (collect at RVD.scala:685) with 1 output partitions 2019-10-08 20:47:48 DAGScheduler: INFO: Final stage: ResultStage 0 (collect at RVD.scala:685) 2019-10-08 20:47:48 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:47:48 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:47:48 DAGScheduler: INFO: Submitting ResultStage 0 (MapPartitionsRDD[5] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:47:48 MemoryStore: INFO: Block broadcast_3 stored as values in memory (estimated size 10.4 KB, free 21.7 GB) 2019-10-08 20:47:48 MemoryStore: INFO: Block broadcast_3_piece0 stored as bytes in memory (estimated size 5.7 KB, free 21.7 GB) 2019-10-08 20:47:48 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:47:48 SparkContext: INFO: Created broadcast 3 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:47:48 DAGScheduler: INFO: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[5] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0)) 2019-10-08 20:47:48 YarnScheduler: INFO: Adding task set 0.0 with 1 tasks 2019-10-08 20:47:48 FairSchedulableBuilder: INFO: Added task set TaskSet_0.0 tasks to pool default 2019-10-08 20:47:48 TaskSetManager: INFO: Starting task 0.0 in stage 0.0 (TID 0, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7664 bytes) 2019-10-08 20:47:49 BlockManagerInfo: INFO: Added broadcast_3_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:47:49 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 28.2 KB, free: 9.5 GB) 2019-10-08 20:47:51 TaskSetManager: INFO: Finished task 0.0 in stage 0.0 (TID 0) in 2782 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/1) 2019-10-08 20:47:51 YarnScheduler: INFO: Removed TaskSet 0.0, whose tasks have all completed, from pool default 2019-10-08 20:47:51 DAGScheduler: INFO: ResultStage 0 (collect at RVD.scala:685) finished in 2.866 s 2019-10-08 20:47:51 DAGScheduler: INFO: Job 0 finished: collect at RVD.scala:685, took 2.972048 s 2019-10-08 20:47:51 root: INFO: is/hail/codegen/generated/C_etypeDecode_4. instruction count: 3 2019-10-08 20:47:51 root: INFO: is/hail/codegen/generated/C_etypeDecode_4.apply instruction count: 7 2019-10-08 20:47:51 root: INFO: is/hail/codegen/generated/C_etypeDecode_4.apply instruction count: 12 2019-10-08 20:47:51 root: INFO: is/hail/codegen/generated/C_etypeDecode_4.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:47:51 root: INFO: is/hail/codegen/generated/C_etypeDecode_4.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:47:52 BlockManagerInfo: INFO: Removed broadcast_3_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:47:52 BlockManagerInfo: INFO: Removed broadcast_3_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_5. instruction count: 3 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_5.apply instruction count: 7 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_5.apply instruction count: 12 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_5.DECODE_o_struct_of_END_TO_o_tuple_of_END_1 instruction count: 14 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6. instruction count: 3 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.apply instruction count: 7 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.apply instruction count: 12 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.DECODE_o_struct_of_o_binaryANDo_float64ANDo_float64ANDo_boolANDo_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int32ANDo_float64ANDo_boolANDo_boolANDo_binaryANDo_boolANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_int32ANDo_binaryANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_boolANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_array_of_o_binaryANDo_array_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_boolANDo_binaryANDo_int32ANDo_binaryANDo_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDENDANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_array_of_o_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryANDo_binaryANDo_boolANDo_boolANDo_binaryANDo_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 979 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_float64_3 instruction count: 5 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_bool_4 instruction count: 5 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_binary_5 instruction count: 9 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_int32_6 instruction count: 5 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_array_of_o_binary_7 instruction count: 54 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDEND_8 instruction count: 337 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_int64_9 instruction count: 5 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.SKIP_o_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64END_10 instruction count: 71 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeDecode_6.INPLACE_DECODE_o_bool_TO_o_bool_11 instruction count: 8 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7. instruction count: 3 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7.apply instruction count: 7 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7.apply instruction count: 11 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7.ENCODE_o_tuple_of_o_stringANDo_boolEND_TO_o_struct_of_o_binaryANDo_boolEND_1 instruction count: 43 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:47:52 root: INFO: is/hail/codegen/generated/C_etypeEncode_7.ENCODE_o_bool_TO_o_bool_3 instruction count: 6 2019-10-08 20:47:52 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:47:52 DAGScheduler: INFO: Got job 1 (collect at RVD.scala:685) with 10 output partitions 2019-10-08 20:47:52 DAGScheduler: INFO: Final stage: ResultStage 1 (collect at RVD.scala:685) 2019-10-08 20:47:52 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:47:52 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:47:52 DAGScheduler: INFO: Submitting ResultStage 1 (MapPartitionsRDD[11] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:47:52 MemoryStore: INFO: Block broadcast_4 stored as values in memory (estimated size 26.7 KB, free 21.7 GB) 2019-10-08 20:47:52 MemoryStore: INFO: Block broadcast_4_piece0 stored as bytes in memory (estimated size 13.1 KB, free 21.7 GB) 2019-10-08 20:47:52 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:47:52 SparkContext: INFO: Created broadcast 4 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:47:52 DAGScheduler: INFO: Submitting 10 missing tasks from ResultStage 1 (MapPartitionsRDD[11] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)) 2019-10-08 20:47:52 YarnScheduler: INFO: Adding task set 1.0 with 10 tasks 2019-10-08 20:47:52 FairSchedulableBuilder: INFO: Added task set TaskSet_1.0 tasks to pool default 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 0.0 in stage 1.0 (TID 1, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 1.0 in stage 1.0 (TID 2, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 1, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 2.0 in stage 1.0 (TID 3, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 2, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 3.0 in stage 1.0 (TID 4, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 3, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 4.0 in stage 1.0 (TID 5, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 4, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 5.0 in stage 1.0 (TID 6, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 5, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 6.0 in stage 1.0 (TID 7, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 6, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 7.0 in stage 1.0 (TID 8, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 7, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:47:52 BlockManagerInfo: INFO: Added broadcast_4_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:33869 (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 8.0 in stage 1.0 (TID 9, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Starting task 9.0 in stage 1.0 (TID 10, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:47:52 TaskSetManager: INFO: Finished task 2.0 in stage 1.0 (TID 3) in 330 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/10) 2019-10-08 20:47:52 TaskSetManager: INFO: Finished task 0.0 in stage 1.0 (TID 1) in 335 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (2/10) 2019-10-08 20:47:52 TaskSetManager: INFO: Finished task 6.0 in stage 1.0 (TID 7) in 337 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (3/10) 2019-10-08 20:47:52 TaskSetManager: INFO: Finished task 4.0 in stage 1.0 (TID 5) in 364 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (4/10) 2019-10-08 20:47:53 TaskSetManager: INFO: Finished task 8.0 in stage 1.0 (TID 9) in 207 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (5/10) 2019-10-08 20:47:53 TaskSetManager: INFO: Finished task 9.0 in stage 1.0 (TID 10) in 338 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (6/10) 2019-10-08 20:47:53 BlockManagerInfo: INFO: Added broadcast_2_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:33869 (size: 28.2 KB, free: 9.5 GB) 2019-10-08 20:47:55 TaskSetManager: INFO: Finished task 1.0 in stage 1.0 (TID 2) in 2773 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (7/10) 2019-10-08 20:47:55 TaskSetManager: INFO: Finished task 3.0 in stage 1.0 (TID 4) in 2773 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (8/10) 2019-10-08 20:47:55 TaskSetManager: INFO: Finished task 5.0 in stage 1.0 (TID 6) in 2774 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (9/10) 2019-10-08 20:47:55 TaskSetManager: INFO: Finished task 7.0 in stage 1.0 (TID 8) in 2779 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (10/10) 2019-10-08 20:47:55 YarnScheduler: INFO: Removed TaskSet 1.0, whose tasks have all completed, from pool default 2019-10-08 20:47:55 DAGScheduler: INFO: ResultStage 1 (collect at RVD.scala:685) finished in 2.795 s 2019-10-08 20:47:55 DAGScheduler: INFO: Job 1 finished: collect at RVD.scala:685, took 2.800618 s 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8. instruction count: 3 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8.apply instruction count: 7 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8.apply instruction count: 12 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8.DECODE_o_struct_of_o_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 71 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C_etypeDecode_8.INPLACE_DECODE_o_bool_TO_o_bool_3 instruction count: 8 2019-10-08 20:47:55 root: INFO: optimize (Compile): before: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_154 (ToDict (ArrayMap __iruid_155 (GetField rows (GetField __iruid_174 (Ref __iruid_172))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_155)) (SelectFields (release) (Ref __iruid_155))))) (Let __iruid_156 (ArrayMap __iruid_157 (GetField rows (GetField __iruid_173 (Ref __iruid_172))) (InsertFields (Ref __iruid_157) None (__uid_3 (ApplyIR get Struct{release:Boolean} (Ref __iruid_154) (MakeStruct (s (GetField s (Ref __iruid_157)))))))) (Let __iruid_158 (ArrayMap __iruid_159 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_156)) (I32 1)) (Let __iruid_160 (ArrayRef (Ref __iruid_156) (Ref __iruid_159)) (InsertFields (SelectFields () (Ref __iruid_160)) None (meta (GetField __uid_3 (Ref __iruid_160)))))) (MakeStruct (rows (ArrayMap __iruid_161 (ArrayFilter __iruid_162 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_158)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_158) (Ref __iruid_162)))) (False))) (ArrayRef (Ref __iruid_158) (Ref __iruid_161)))))))))))) 2019-10-08 20:47:55 root: INFO: optimize (Compile): after: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_225 (ToDict (ArrayMap __iruid_226 (GetField rows (GetField __iruid_174 (Ref __iruid_172))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_226)) (SelectFields (release) (Ref __iruid_226))))) (Let __iruid_227 (ArrayMap __iruid_228 (GetField rows (GetField __iruid_173 (Ref __iruid_172))) (InsertFields (Ref __iruid_228) None (__uid_3 (ApplyIR get Struct{release:Boolean} (Ref __iruid_225) (MakeStruct (s (GetField s (Ref __iruid_228)))))))) (Let __iruid_229 (ArrayMap __iruid_230 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_227)) (I32 1)) (Let __iruid_231 (ArrayRef (Ref __iruid_227) (Ref __iruid_230)) (InsertFields (SelectFields () (Ref __iruid_231)) None (meta (GetField __uid_3 (Ref __iruid_231)))))) (MakeStruct (rows (ArrayMap __iruid_232 (ArrayFilter __iruid_233 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_229)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_229) (Ref __iruid_233)))) (False))) (ArrayRef (Ref __iruid_229) (Ref __iruid_232)))))))))))) 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10. instruction count: 3 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.apply instruction count: 11 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.apply instruction count: 14 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.method_1 instruction count: 110 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.method_2 instruction count: 45 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.method_3 instruction count: 92 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C10.method_4 instruction count: 105 2019-10-08 20:47:55 MemoryStore: INFO: Block broadcast_5 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:47:55 MemoryStore: INFO: Block broadcast_5_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:47:55 BlockManagerInfo: INFO: Added broadcast_5_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:47:55 SparkContext: INFO: Created broadcast 5 from broadcast at SparkBackend.scala:21 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9. instruction count: 3 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.apply instruction count: 45 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.apply instruction count: 28 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_1 instruction count: 1890 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_2 instruction count: 99 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_3 instruction count: 83 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_4 instruction count: 106 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_5 instruction count: 64 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_6 instruction count: 563 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_7 instruction count: 87 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_8 instruction count: 92 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_9 instruction count: 105 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_10 instruction count: 37 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.method_11 instruction count: 725 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.setPartitionIndex instruction count: 14 2019-10-08 20:47:55 root: INFO: is/hail/codegen/generated/C9.addPartitionRegion instruction count: 6 2019-10-08 20:47:55 root: INFO: Time taken for CompileAndEvaluate -- first pass: 120.126ms 2019-10-08 20:47:55 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 216.357ms 2019-10-08 20:47:55 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 7.629s 2019-10-08 20:47:55 root: INFO: Time taken for CompileAndEvaluate -- compile: 202.375ms 2019-10-08 20:47:55 root: INFO: Time taken for CompileAndEvaluate -- runtime: 175.046ms 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 180: (TableCount (MatrixRowsTable (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_8" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_7" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_7 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_9 (GetField __uid_8 (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_9))) (age_hist_het (GetField age_hist_het (Ref __uid_9))) (age_hist_hom (GetField age_hist_hom (Ref __uid_9))) (popmax (GetField popmax (Ref __uid_9))) (faf (GetField faf (Ref __uid_9))) (lcr (GetField lcr (Ref __uid_9))) (decoy (GetField decoy (Ref __uid_9))) (segdup (GetField segdup (Ref __uid_9))) (nonpar (GetField nonpar (Ref __uid_9))) (variant_type (GetField variant_type (Ref __uid_9))) (allele_type (GetField allele_type (Ref __uid_9))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_9))) (was_mixed (GetField was_mixed (Ref __uid_9))) (has_star (GetField has_star (Ref __uid_9))) (qd (GetField qd (Ref __uid_9))) (pab_max (GetField pab_max (Ref __uid_9))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_9))) (info_SOR (GetField info_SOR (Ref __uid_9))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_9))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_9))) (info_FS (GetField info_FS (Ref __uid_9))) (info_QD (GetField info_QD (Ref __uid_9))) (info_MQ (GetField info_MQ (Ref __uid_9))) (info_DP (GetField info_DP (Ref __uid_9))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_9))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_9))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_9))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_9))) (omni (GetField omni (Ref __uid_9))) (mills (GetField mills (Ref __uid_9))) (tp (GetField tp (Ref __uid_9))) (rf_train (GetField rf_train (Ref __uid_9))) (rf_label (GetField rf_label (Ref __uid_9))) (rf_probability (GetField rf_probability (Ref __uid_9))) (rank (GetField rank (Ref __uid_9))) (was_split (GetField was_split (Ref __uid_9))) (singleton (GetField singleton (Ref __uid_9))) (_score (GetField _score (Ref __uid_9))) (_singleton (GetField _singleton (Ref __uid_9))) (biallelic_rank (GetField biallelic_rank (Ref __uid_9))) (singleton_rank (GetField singleton_rank (Ref __uid_9))) (n_nonref (GetField n_nonref (Ref __uid_9))) (score (GetField score (Ref __uid_9))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_9))) (adj_rank (GetField adj_rank (Ref __uid_9))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_9))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_9))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_9))) (filters (GetField filters (Ref __uid_9))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_9))) (gq_hist_all (GetField gq_hist_all (Ref __uid_9))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_9))) (dp_hist_all (GetField dp_hist_all (Ref __uid_9))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_9))) (qual (GetField qual (Ref __uid_9))) (vep (GetField vep (Ref __uid_9))) (allele_info (GetField allele_info (Ref __uid_9))) (rsid (GetField rsid (Ref __uid_9)))))) (Let __uid_10 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_10))) (freq_meta (GetField freq_meta (Ref __uid_10))) (freq_index_dict (GetField freq_index_dict (Ref __uid_10))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_10))) (age_index_dict (GetField age_index_dict (Ref __uid_10))) (faf_index_dict (GetField faf_index_dict (Ref __uid_10))) (age_distribution (GetField age_distribution (Ref __uid_10)))))))) 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 1: (I64 290745715) 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 1: (I64 290745715) 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 1: (I64 290745715) 2019-10-08 20:48:00 root: INFO: optimize (Compile): before: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:48:00 root: INFO: optimize (Compile): after: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:48:00 MemoryStore: INFO: Block broadcast_6 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:48:00 MemoryStore: INFO: Block broadcast_6_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:48:00 BlockManagerInfo: INFO: Added broadcast_6_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:48:00 SparkContext: INFO: Created broadcast 6 from broadcast at SparkBackend.scala:21 2019-10-08 20:48:00 root: INFO: is/hail/codegen/generated/C11. instruction count: 3 2019-10-08 20:48:00 root: INFO: is/hail/codegen/generated/C11.apply instruction count: 53 2019-10-08 20:48:00 root: INFO: is/hail/codegen/generated/C11.apply instruction count: 28 2019-10-08 20:48:00 root: INFO: is/hail/codegen/generated/C11.setPartitionIndex instruction count: 14 2019-10-08 20:48:00 root: INFO: is/hail/codegen/generated/C11.addPartitionRegion instruction count: 6 2019-10-08 20:48:00 root: INFO: Time taken for CompileAndEvaluate -- first pass: 15.721ms 2019-10-08 20:48:00 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 0.354ms 2019-10-08 20:48:00 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 0.110ms 2019-10-08 20:48:00 root: INFO: Time taken for CompileAndEvaluate -- compile: 13.279ms 2019-10-08 20:48:00 root: INFO: Time taken for CompileAndEvaluate -- runtime: 1.453ms 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 180: (TableCount (MatrixColsTable (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_8" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_7" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_7 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_9 (GetField __uid_8 (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_9))) (age_hist_het (GetField age_hist_het (Ref __uid_9))) (age_hist_hom (GetField age_hist_hom (Ref __uid_9))) (popmax (GetField popmax (Ref __uid_9))) (faf (GetField faf (Ref __uid_9))) (lcr (GetField lcr (Ref __uid_9))) (decoy (GetField decoy (Ref __uid_9))) (segdup (GetField segdup (Ref __uid_9))) (nonpar (GetField nonpar (Ref __uid_9))) (variant_type (GetField variant_type (Ref __uid_9))) (allele_type (GetField allele_type (Ref __uid_9))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_9))) (was_mixed (GetField was_mixed (Ref __uid_9))) (has_star (GetField has_star (Ref __uid_9))) (qd (GetField qd (Ref __uid_9))) (pab_max (GetField pab_max (Ref __uid_9))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_9))) (info_SOR (GetField info_SOR (Ref __uid_9))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_9))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_9))) (info_FS (GetField info_FS (Ref __uid_9))) (info_QD (GetField info_QD (Ref __uid_9))) (info_MQ (GetField info_MQ (Ref __uid_9))) (info_DP (GetField info_DP (Ref __uid_9))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_9))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_9))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_9))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_9))) (omni (GetField omni (Ref __uid_9))) (mills (GetField mills (Ref __uid_9))) (tp (GetField tp (Ref __uid_9))) (rf_train (GetField rf_train (Ref __uid_9))) (rf_label (GetField rf_label (Ref __uid_9))) (rf_probability (GetField rf_probability (Ref __uid_9))) (rank (GetField rank (Ref __uid_9))) (was_split (GetField was_split (Ref __uid_9))) (singleton (GetField singleton (Ref __uid_9))) (_score (GetField _score (Ref __uid_9))) (_singleton (GetField _singleton (Ref __uid_9))) (biallelic_rank (GetField biallelic_rank (Ref __uid_9))) (singleton_rank (GetField singleton_rank (Ref __uid_9))) (n_nonref (GetField n_nonref (Ref __uid_9))) (score (GetField score (Ref __uid_9))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_9))) (adj_rank (GetField adj_rank (Ref __uid_9))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_9))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_9))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_9))) (filters (GetField filters (Ref __uid_9))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_9))) (gq_hist_all (GetField gq_hist_all (Ref __uid_9))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_9))) (dp_hist_all (GetField dp_hist_all (Ref __uid_9))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_9))) (qual (GetField qual (Ref __uid_9))) (vep (GetField vep (Ref __uid_9))) (allele_info (GetField allele_info (Ref __uid_9))) (rsid (GetField rsid (Ref __uid_9)))))) (Let __uid_10 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_10))) (freq_meta (GetField freq_meta (Ref __uid_10))) (freq_index_dict (GetField freq_index_dict (Ref __uid_10))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_10))) (age_index_dict (GetField age_index_dict (Ref __uid_10))) (faf_index_dict (GetField faf_index_dict (Ref __uid_10))) (age_distribution (GetField age_distribution (Ref __uid_10)))))))) 2019-10-08 20:48:00 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 25: (TableCount (MatrixColsTable (MatrixFilterCols (MatrixMapCols () (MatrixAnnotateColsTable "__uid_7" (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/genomes/gnomad.genomes.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/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_7 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))))) 2019-10-08 20:48:01 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 155: (TableCount (TableKeyBy () False (TableParallelize None (Let __cols_and_globals (TableGetGlobals (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/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (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_250 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_250)) (SelectFields (release) (Ref __iruid_250))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_249 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_249) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_249)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_254 (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_254)) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_7 (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)))))))) (MakeStruct (rows (GetField __cols (Ref __cols_and_globals))) (global (SelectFields () (Ref __cols_and_globals)))))))) 2019-10-08 20:48:01 root: INFO: Prune: MakeStruct: eliminating field 'global' 2019-10-08 20:48:01 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 61: (Cast Int64 (ArrayLen (GetField rows (Let __iruid_368 (ToDict (ArrayMap __iruid_369 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_369)) (SelectFields (release) (Ref __iruid_369))))) (Let __iruid_370 (ArrayMap __iruid_371 (GetField rows (TableCollect (TableRead Table{global:Struct{},key:[],row:Struct{s:String}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}"))) (InsertFields (Ref __iruid_371) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __iruid_368) (MakeStruct (s (GetField s (Ref __iruid_371)))))))) (Let __iruid_372 (ArrayMap __iruid_373 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_370)) (I32 1)) (Let __iruid_374 (ArrayRef (Ref __iruid_370) (Ref __iruid_373)) (InsertFields (SelectFields () (Ref __iruid_374)) None (meta (GetField __uid_7 (Ref __iruid_374)))))) (MakeStruct (rows (ArrayMap __iruid_375 (ArrayFilter __iruid_376 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_372)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_372) (Ref __iruid_376)))) (False))) (ArrayRef (Ref __iruid_372) (Ref __iruid_375))))))))))) 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_12. instruction count: 3 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_12.apply instruction count: 7 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_12.apply instruction count: 12 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_12.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_13. instruction count: 3 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_13.apply instruction count: 7 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_13.apply instruction count: 12 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_13.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeDecode_13.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeEncode_14. instruction count: 3 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeEncode_14.apply instruction count: 7 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeEncode_14.apply instruction count: 11 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeEncode_14.ENCODE_o_tuple_of_o_stringEND_TO_o_struct_of_o_binaryEND_1 instruction count: 25 2019-10-08 20:48:01 root: INFO: is/hail/codegen/generated/C_etypeEncode_14.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:48:02 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:48:02 DAGScheduler: INFO: Got job 2 (collect at RVD.scala:685) with 1 output partitions 2019-10-08 20:48:02 DAGScheduler: INFO: Final stage: ResultStage 2 (collect at RVD.scala:685) 2019-10-08 20:48:02 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:48:02 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:48:02 DAGScheduler: INFO: Submitting ResultStage 2 (MapPartitionsRDD[17] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:48:02 MemoryStore: INFO: Block broadcast_7 stored as values in memory (estimated size 10.5 KB, free 21.7 GB) 2019-10-08 20:48:02 MemoryStore: INFO: Block broadcast_7_piece0 stored as bytes in memory (estimated size 5.7 KB, free 21.7 GB) 2019-10-08 20:48:02 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:48:02 SparkContext: INFO: Created broadcast 7 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:48:02 DAGScheduler: INFO: Submitting 1 missing tasks from ResultStage 2 (MapPartitionsRDD[17] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0)) 2019-10-08 20:48:02 YarnScheduler: INFO: Adding task set 2.0 with 1 tasks 2019-10-08 20:48:02 FairSchedulableBuilder: INFO: Added task set TaskSet_2.0 tasks to pool default 2019-10-08 20:48:02 TaskSetManager: INFO: Starting task 0.0 in stage 2.0 (TID 11, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7664 bytes) 2019-10-08 20:48:02 BlockManagerInfo: INFO: Added broadcast_7_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:48:02 TaskSetManager: INFO: Finished task 0.0 in stage 2.0 (TID 11) in 454 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/1) 2019-10-08 20:48:02 YarnScheduler: INFO: Removed TaskSet 2.0, whose tasks have all completed, from pool default 2019-10-08 20:48:02 DAGScheduler: INFO: ResultStage 2 (collect at RVD.scala:685) finished in 0.475 s 2019-10-08 20:48:02 DAGScheduler: INFO: Job 2 finished: collect at RVD.scala:685, took 0.480331 s 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_15. instruction count: 3 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_15.apply instruction count: 7 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_15.apply instruction count: 12 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_15.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_15.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_16. instruction count: 3 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_16.apply instruction count: 7 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_16.apply instruction count: 12 2019-10-08 20:48:02 root: INFO: is/hail/codegen/generated/C_etypeDecode_16.DECODE_o_struct_of_END_TO_o_tuple_of_END_1 instruction count: 14 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17. instruction count: 3 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.apply instruction count: 7 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.apply instruction count: 12 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.DECODE_o_struct_of_o_binaryANDo_float64ANDo_float64ANDo_boolANDo_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int32ANDo_float64ANDo_boolANDo_boolANDo_binaryANDo_boolANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_int32ANDo_binaryANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_boolANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_array_of_o_binaryANDo_array_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_boolANDo_binaryANDo_int32ANDo_binaryANDo_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDENDANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_array_of_o_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryANDo_binaryANDo_boolANDo_boolANDo_binaryANDo_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 979 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_float64_3 instruction count: 5 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_bool_4 instruction count: 5 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_binary_5 instruction count: 9 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_int32_6 instruction count: 5 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_array_of_o_binary_7 instruction count: 54 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDEND_8 instruction count: 337 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_int64_9 instruction count: 5 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.SKIP_o_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64END_10 instruction count: 71 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_17.INPLACE_DECODE_o_bool_TO_o_bool_11 instruction count: 8 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18. instruction count: 3 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.apply instruction count: 7 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.apply instruction count: 11 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.ENCODE_o_tuple_of_o_stringANDo_boolEND_TO_o_struct_of_o_binaryANDo_boolEND_1 instruction count: 43 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeEncode_18.ENCODE_o_bool_TO_o_bool_3 instruction count: 6 2019-10-08 20:48:03 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:48:03 DAGScheduler: INFO: Got job 3 (collect at RVD.scala:685) with 10 output partitions 2019-10-08 20:48:03 DAGScheduler: INFO: Final stage: ResultStage 3 (collect at RVD.scala:685) 2019-10-08 20:48:03 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:48:03 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:48:03 DAGScheduler: INFO: Submitting ResultStage 3 (MapPartitionsRDD[23] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:48:03 MemoryStore: INFO: Block broadcast_8 stored as values in memory (estimated size 26.7 KB, free 21.7 GB) 2019-10-08 20:48:03 MemoryStore: INFO: Block broadcast_8_piece0 stored as bytes in memory (estimated size 13.1 KB, free 21.7 GB) 2019-10-08 20:48:03 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:48:03 SparkContext: INFO: Created broadcast 8 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:48:03 DAGScheduler: INFO: Submitting 10 missing tasks from ResultStage 3 (MapPartitionsRDD[23] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)) 2019-10-08 20:48:03 YarnScheduler: INFO: Adding task set 3.0 with 10 tasks 2019-10-08 20:48:03 FairSchedulableBuilder: INFO: Added task set TaskSet_3.0 tasks to pool default 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 0.0 in stage 3.0 (TID 12, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 1.0 in stage 3.0 (TID 13, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 1, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 2.0 in stage 3.0 (TID 14, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 2, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 3.0 in stage 3.0 (TID 15, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 3, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 4.0 in stage 3.0 (TID 16, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 4, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 5.0 in stage 3.0 (TID 17, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 5, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 6.0 in stage 3.0 (TID 18, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 6, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 7.0 in stage 3.0 (TID 19, mw-w-0.c.broad-mpg-gnomad.internal, executor 2, partition 7, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:03 BlockManagerInfo: INFO: Added broadcast_8_piece0 in memory on mw-w-0.c.broad-mpg-gnomad.internal:33869 (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 8.0 in stage 3.0 (TID 20, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Starting task 9.0 in stage 3.0 (TID 21, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 6.0 in stage 3.0 (TID 18) in 193 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 2.0 in stage 3.0 (TID 14) in 195 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (2/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 4.0 in stage 3.0 (TID 16) in 208 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (3/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 0.0 in stage 3.0 (TID 12) in 257 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (4/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 1.0 in stage 3.0 (TID 13) in 333 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (5/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 3.0 in stage 3.0 (TID 15) in 333 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (6/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 8.0 in stage 3.0 (TID 20) in 162 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (7/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 9.0 in stage 3.0 (TID 21) in 165 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (8/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 7.0 in stage 3.0 (TID 19) in 370 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (9/10) 2019-10-08 20:48:03 TaskSetManager: INFO: Finished task 5.0 in stage 3.0 (TID 17) in 375 ms on mw-w-0.c.broad-mpg-gnomad.internal (executor 2) (10/10) 2019-10-08 20:48:03 YarnScheduler: INFO: Removed TaskSet 3.0, whose tasks have all completed, from pool default 2019-10-08 20:48:03 DAGScheduler: INFO: ResultStage 3 (collect at RVD.scala:685) finished in 0.387 s 2019-10-08 20:48:03 DAGScheduler: INFO: Job 3 finished: collect at RVD.scala:685, took 0.391953 s 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19. instruction count: 3 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.apply instruction count: 7 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.apply instruction count: 12 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.DECODE_o_struct_of_o_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 71 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C_etypeDecode_19.INPLACE_DECODE_o_bool_TO_o_bool_3 instruction count: 8 2019-10-08 20:48:03 root: INFO: optimize (Compile): before: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_368 (ToDict (ArrayMap __iruid_369 (GetField rows (GetField __iruid_388 (Ref __iruid_386))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_369)) (SelectFields (release) (Ref __iruid_369))))) (Let __iruid_370 (ArrayMap __iruid_371 (GetField rows (GetField __iruid_387 (Ref __iruid_386))) (InsertFields (Ref __iruid_371) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __iruid_368) (MakeStruct (s (GetField s (Ref __iruid_371)))))))) (Let __iruid_372 (ArrayMap __iruid_373 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_370)) (I32 1)) (Let __iruid_374 (ArrayRef (Ref __iruid_370) (Ref __iruid_373)) (InsertFields (SelectFields () (Ref __iruid_374)) None (meta (GetField __uid_7 (Ref __iruid_374)))))) (MakeStruct (rows (ArrayMap __iruid_375 (ArrayFilter __iruid_376 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_372)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_372) (Ref __iruid_376)))) (False))) (ArrayRef (Ref __iruid_372) (Ref __iruid_375)))))))))))) 2019-10-08 20:48:03 root: INFO: optimize (Compile): after: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_439 (ToDict (ArrayMap __iruid_440 (GetField rows (GetField __iruid_388 (Ref __iruid_386))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_440)) (SelectFields (release) (Ref __iruid_440))))) (Let __iruid_441 (ArrayMap __iruid_442 (GetField rows (GetField __iruid_387 (Ref __iruid_386))) (InsertFields (Ref __iruid_442) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __iruid_439) (MakeStruct (s (GetField s (Ref __iruid_442)))))))) (Let __iruid_443 (ArrayMap __iruid_444 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_441)) (I32 1)) (Let __iruid_445 (ArrayRef (Ref __iruid_441) (Ref __iruid_444)) (InsertFields (SelectFields () (Ref __iruid_445)) None (meta (GetField __uid_7 (Ref __iruid_445)))))) (MakeStruct (rows (ArrayMap __iruid_446 (ArrayFilter __iruid_447 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_443)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_443) (Ref __iruid_447)))) (False))) (ArrayRef (Ref __iruid_443) (Ref __iruid_446)))))))))))) 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21. instruction count: 3 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.apply instruction count: 11 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.apply instruction count: 14 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.method_1 instruction count: 110 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.method_2 instruction count: 45 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.method_3 instruction count: 92 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C21.method_4 instruction count: 105 2019-10-08 20:48:03 MemoryStore: INFO: Block broadcast_9 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:48:03 MemoryStore: INFO: Block broadcast_9_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:48:03 BlockManagerInfo: INFO: Added broadcast_9_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:48:03 SparkContext: INFO: Created broadcast 9 from broadcast at SparkBackend.scala:21 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20. instruction count: 3 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.apply instruction count: 45 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.apply instruction count: 28 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_1 instruction count: 1890 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_2 instruction count: 99 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_3 instruction count: 83 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_4 instruction count: 106 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_5 instruction count: 64 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_6 instruction count: 563 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_7 instruction count: 87 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_8 instruction count: 92 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_9 instruction count: 105 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_10 instruction count: 37 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.method_11 instruction count: 725 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.setPartitionIndex instruction count: 14 2019-10-08 20:48:03 root: INFO: is/hail/codegen/generated/C20.addPartitionRegion instruction count: 6 2019-10-08 20:48:03 root: INFO: Time taken for CompileAndEvaluate -- first pass: 39.902ms 2019-10-08 20:48:03 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 123.618ms 2019-10-08 20:48:03 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 1.871s 2019-10-08 20:48:03 root: INFO: Time taken for CompileAndEvaluate -- compile: 81.468ms 2019-10-08 20:48:03 root: INFO: Time taken for CompileAndEvaluate -- runtime: 136.260ms 2019-10-08 20:48:24 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 441: (TableCount (MatrixRowsTable (MatrixMapRows (MatrixFilterRows (MatrixMapRows (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_8" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_7" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_7 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_9 (GetField __uid_8 (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_9))) (age_hist_het (GetField age_hist_het (Ref __uid_9))) (age_hist_hom (GetField age_hist_hom (Ref __uid_9))) (popmax (GetField popmax (Ref __uid_9))) (faf (GetField faf (Ref __uid_9))) (lcr (GetField lcr (Ref __uid_9))) (decoy (GetField decoy (Ref __uid_9))) (segdup (GetField segdup (Ref __uid_9))) (nonpar (GetField nonpar (Ref __uid_9))) (variant_type (GetField variant_type (Ref __uid_9))) (allele_type (GetField allele_type (Ref __uid_9))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_9))) (was_mixed (GetField was_mixed (Ref __uid_9))) (has_star (GetField has_star (Ref __uid_9))) (qd (GetField qd (Ref __uid_9))) (pab_max (GetField pab_max (Ref __uid_9))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_9))) (info_SOR (GetField info_SOR (Ref __uid_9))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_9))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_9))) (info_FS (GetField info_FS (Ref __uid_9))) (info_QD (GetField info_QD (Ref __uid_9))) (info_MQ (GetField info_MQ (Ref __uid_9))) (info_DP (GetField info_DP (Ref __uid_9))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_9))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_9))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_9))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_9))) (omni (GetField omni (Ref __uid_9))) (mills (GetField mills (Ref __uid_9))) (tp (GetField tp (Ref __uid_9))) (rf_train (GetField rf_train (Ref __uid_9))) (rf_label (GetField rf_label (Ref __uid_9))) (rf_probability (GetField rf_probability (Ref __uid_9))) (rank (GetField rank (Ref __uid_9))) (was_split (GetField was_split (Ref __uid_9))) (singleton (GetField singleton (Ref __uid_9))) (_score (GetField _score (Ref __uid_9))) (_singleton (GetField _singleton (Ref __uid_9))) (biallelic_rank (GetField biallelic_rank (Ref __uid_9))) (singleton_rank (GetField singleton_rank (Ref __uid_9))) (n_nonref (GetField n_nonref (Ref __uid_9))) (score (GetField score (Ref __uid_9))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_9))) (adj_rank (GetField adj_rank (Ref __uid_9))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_9))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_9))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_9))) (filters (GetField filters (Ref __uid_9))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_9))) (gq_hist_all (GetField gq_hist_all (Ref __uid_9))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_9))) (dp_hist_all (GetField dp_hist_all (Ref __uid_9))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_9))) (qual (GetField qual (Ref __uid_9))) (vep (GetField vep (Ref __uid_9))) (allele_info (GetField allele_info (Ref __uid_9))) (rsid (GetField rsid (Ref __uid_9)))))) (Let __uid_10 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_10))) (freq_meta (GetField freq_meta (Ref __uid_10))) (freq_index_dict (GetField freq_index_dict (Ref __uid_10))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_10))) (age_index_dict (GetField age_index_dict (Ref __uid_10))) (faf_index_dict (GetField faf_index_dict (Ref __uid_10))) (age_distribution (GetField age_distribution (Ref __uid_10)))))) (InsertFields (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (freq (GetField freq (Ref va))) (age_hist_het (GetField age_hist_het (Ref va))) (age_hist_hom (GetField age_hist_hom (Ref va))) (popmax (GetField popmax (Ref va))) (faf (GetField faf (Ref va))) (lcr (GetField lcr (Ref va))) (decoy (GetField decoy (Ref va))) (segdup (GetField segdup (Ref va))) (nonpar (GetField nonpar (Ref va))) (variant_type (GetField variant_type (Ref va))) (allele_type (GetField allele_type (Ref va))) (n_alt_alleles (GetField n_alt_alleles (Ref va))) (was_mixed (GetField was_mixed (Ref va))) (has_star (GetField has_star (Ref va))) (qd (GetField qd (Ref va))) (pab_max (GetField pab_max (Ref va))) (info_MQRankSum (GetField info_MQRankSum (Ref va))) (info_SOR (GetField info_SOR (Ref va))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref va))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref va))) (info_FS (GetField info_FS (Ref va))) (info_QD (GetField info_QD (Ref va))) (info_MQ (GetField info_MQ (Ref va))) (info_DP (GetField info_DP (Ref va))) (transmitted_singleton (GetField transmitted_singleton (Ref va))) (fail_hard_filters (GetField fail_hard_filters (Ref va))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref va))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref va))) (omni (GetField omni (Ref va))) (mills (GetField mills (Ref va))) (tp (GetField tp (Ref va))) (rf_train (GetField rf_train (Ref va))) (rf_label (GetField rf_label (Ref va))) (rf_probability (GetField rf_probability (Ref va))) (rank (GetField rank (Ref va))) (was_split (GetField was_split (Ref va))) (singleton (GetField singleton (Ref va))) (_score (GetField _score (Ref va))) (_singleton (GetField _singleton (Ref va))) (biallelic_rank (GetField biallelic_rank (Ref va))) (singleton_rank (GetField singleton_rank (Ref va))) (n_nonref (GetField n_nonref (Ref va))) (score (GetField score (Ref va))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref va))) (adj_rank (GetField adj_rank (Ref va))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref va))) (adj_singleton_rank (GetField adj_singleton_rank (Ref va))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref va))) (filters (GetField filters (Ref va))) (gq_hist_alt (GetField gq_hist_alt (Ref va))) (gq_hist_all (GetField gq_hist_all (Ref va))) (dp_hist_alt (GetField dp_hist_alt (Ref va))) (dp_hist_all (GetField dp_hist_all (Ref va))) (ab_hist_alt (GetField ab_hist_alt (Ref va))) (qual (GetField qual (Ref va))) (vep (GetField vep (Ref va))) (allele_info (GetField allele_info (Ref va))) (rsid (GetField rsid (Ref va)))) None (__uid_11 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (ApplyIR toInt64 Int64 (I32 0)))))) (Coalesce (GetField __uid_11 (Ref va)) (False))) (SelectFields (locus alleles freq age_hist_het age_hist_hom popmax faf lcr decoy segdup nonpar variant_type allele_type n_alt_alleles was_mixed has_star qd pab_max info_MQRankSum info_SOR info_InbreedingCoeff info_ReadPosRankSum info_FS info_QD info_MQ info_DP transmitted_singleton fail_hard_filters info_POSITIVE_TRAIN_SITE info_NEGATIVE_TRAIN_SITE omni mills tp rf_train rf_label rf_probability rank was_split singleton _score _singleton biallelic_rank singleton_rank n_nonref score adj_biallelic_singleton_rank adj_rank adj_biallelic_rank adj_singleton_rank biallelic_singleton_rank filters gq_hist_alt gq_hist_all dp_hist_alt dp_hist_all ab_hist_alt qual vep allele_info rsid) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (freq (GetField freq (Ref va))) (age_hist_het (GetField age_hist_het (Ref va))) (age_hist_hom (GetField age_hist_hom (Ref va))) (popmax (GetField popmax (Ref va))) (faf (GetField faf (Ref va))) (lcr (GetField lcr (Ref va))) (decoy (GetField decoy (Ref va))) (segdup (GetField segdup (Ref va))) (nonpar (GetField nonpar (Ref va))) (variant_type (GetField variant_type (Ref va))) (allele_type (GetField allele_type (Ref va))) (n_alt_alleles (GetField n_alt_alleles (Ref va))) (was_mixed (GetField was_mixed (Ref va))) (has_star (GetField has_star (Ref va))) (qd (GetField qd (Ref va))) (pab_max (GetField pab_max (Ref va))) (info_MQRankSum (GetField info_MQRankSum (Ref va))) (info_SOR (GetField info_SOR (Ref va))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref va))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref va))) (info_FS (GetField info_FS (Ref va))) (info_QD (GetField info_QD (Ref va))) (info_MQ (GetField info_MQ (Ref va))) (info_DP (GetField info_DP (Ref va))) (transmitted_singleton (GetField transmitted_singleton (Ref va))) (fail_hard_filters (GetField fail_hard_filters (Ref va))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref va))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref va))) (omni (GetField omni (Ref va))) (mills (GetField mills (Ref va))) (tp (GetField tp (Ref va))) (rf_train (GetField rf_train (Ref va))) (rf_label (GetField rf_label (Ref va))) (rf_probability (GetField rf_probability (Ref va))) (rank (GetField rank (Ref va))) (was_split (GetField was_split (Ref va))) (singleton (GetField singleton (Ref va))) (_score (GetField _score (Ref va))) (_singleton (GetField _singleton (Ref va))) (biallelic_rank (GetField biallelic_rank (Ref va))) (singleton_rank (GetField singleton_rank (Ref va))) (n_nonref (GetField n_nonref (Ref va))) (score (GetField score (Ref va))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref va))) (adj_rank (GetField adj_rank (Ref va))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref va))) (adj_singleton_rank (GetField adj_singleton_rank (Ref va))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref va))) (filters (GetField filters (Ref va))) (gq_hist_alt (GetField gq_hist_alt (Ref va))) (gq_hist_all (GetField gq_hist_all (Ref va))) (dp_hist_alt (GetField dp_hist_alt (Ref va))) (dp_hist_all (GetField dp_hist_all (Ref va))) (ab_hist_alt (GetField ab_hist_alt (Ref va))) (qual (GetField qual (Ref va))) (vep (GetField vep (Ref va))) (allele_info (GetField allele_info (Ref va))) (rsid (GetField rsid (Ref va))) (__uid_11 (GetField __uid_11 (Ref va)))))))) 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'freq' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'age_hist_het' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'age_hist_hom' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'popmax' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'faf' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'lcr' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'decoy' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'segdup' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'nonpar' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'variant_type' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'allele_type' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'n_alt_alleles' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'was_mixed' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'has_star' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'qd' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'pab_max' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_MQRankSum' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_SOR' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_FS' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_QD' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_MQ' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_DP' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'transmitted_singleton' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'fail_hard_filters' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'omni' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'mills' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'tp' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rf_train' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rf_label' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rf_probability' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'was_split' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'singleton' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field '_score' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field '_singleton' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'n_nonref' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'score' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'adj_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'adj_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'filters' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'ab_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'qual' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'vep' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'allele_info' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rsid' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'rf' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'freq_meta' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'freq_index_dict' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'popmax_index_dict' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'age_index_dict' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'faf_index_dict' 2019-10-08 20:48:24 root: INFO: Prune: InsertFields: eliminating field 'age_distribution' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'freq' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_het' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_hom' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'popmax' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'faf' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'lcr' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'decoy' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'segdup' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'nonpar' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'variant_type' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'allele_type' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'n_alt_alleles' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'was_mixed' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'has_star' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'qd' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'pab_max' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_MQRankSum' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_SOR' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_FS' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_QD' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_MQ' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_DP' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'transmitted_singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'fail_hard_filters' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'omni' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'mills' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'tp' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_train' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_label' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_probability' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'was_split' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field '_score' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field '_singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'n_nonref' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'score' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'filters' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'ab_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'qual' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'vep' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'allele_info' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rsid' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'locus' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'alleles' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'freq' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_het' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_hom' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'popmax' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'faf' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'lcr' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'decoy' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'segdup' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'nonpar' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'variant_type' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'allele_type' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'n_alt_alleles' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'was_mixed' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'has_star' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'qd' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'pab_max' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_MQRankSum' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_SOR' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_FS' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_QD' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_MQ' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_DP' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'transmitted_singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'fail_hard_filters' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'omni' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'mills' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'tp' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_train' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_label' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rf_probability' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'was_split' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field '_score' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field '_singleton' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'n_nonref' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'score' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'adj_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'filters' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_all' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'ab_hist_alt' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'qual' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'vep' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'allele_info' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'rsid' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'locus' 2019-10-08 20:48:24 root: INFO: Prune: MakeStruct: eliminating field 'alleles' 2019-10-08 20:48:24 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 43: (TableCount (MatrixRowsTable (MatrixMapRows (MatrixKeyRowsBy () False (MatrixFilterRows (MatrixMapRows (MatrixKeyRowsBy () False (MatrixFilterCols (MatrixMapCols () (MatrixAnnotateColsTable "__uid_7" (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{GT:Call,adj:Boolean}} False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt\",\"_spec\":null}") (Coalesce (GetField adj (Ref g)) (False))) (SelectFields (GT) (Ref g))) (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_7 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False)))) (MakeStruct (__uid_11 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (I64 0))))) (Coalesce (GetField __uid_11 (Ref va)) (False)))) (Literal Struct{} )))) 2019-10-08 20:48:25 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 201: (TableCount (TableMapRows (TableMapGlobals (TableMapRows (TableKeyBy () False (TableFilter (TableMapRows (TableKeyBy () False (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{GT:Call,adj:Boolean}]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (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{GT:Call,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 (GT) (Ref g)))))))) (Let __dictfield (ToDict (ArrayMap __iruid_466 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_466)) (SelectFields (release) (Ref __iruid_466))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_465 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_465) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_465)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_470 (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_470)) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_7 (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)))))))) (InsertFields (ArrayAgg i (ArrayFilter i (ArrayRange (I32 0) (ArrayLen (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (I32 1)) (ApplyUnaryPrimOp Bang (IsNA (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i))))) (AggLet sa False (ArrayRef (GetField __cols (Ref global)) (Ref i)) (AggLet g False (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i)) (MakeStruct (__uid_11 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (I64 0))))))) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))))) (Coalesce (GetField __uid_11 (SelectFields (__uid_11) (Ref row))) (False)))) (InsertFields (Literal Struct{} ) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))))) (SelectFields () (Ref global))) (SelectFields () (Ref row)))) 2019-10-08 20:48:25 root: INFO: Prune: InsertFields: eliminating field '__cols' 2019-10-08 20:48:25 root: INFO: Prune: InsertFields: eliminating field '__cols' 2019-10-08 20:48:25 root: INFO: Prune: InsertFields: eliminating field 'the entries! [877f12a8827e18f61222c6c8c5fb04a8]' 2019-10-08 20:48:25 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 142: (TableCount (TableFilter (TableMapRows (TableKeyBy () False (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,adj:Boolean}]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (Let __iruid_562 (ArrayMap __iruid_563 (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let __iruid_564 (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_563)) (If (Coalesce (GetField adj (Ref __iruid_564)) (False)) (Ref __iruid_564) (NA Struct{GT:Call,adj:Boolean})))) (InsertFields (Ref row) ("locus" "alleles" "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap __iruid_565 (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (SelectFields (GT) (ArrayRef (Ref __iruid_562) (Ref __iruid_565)))))))) (Let __iruid_566 (ToDict (ArrayMap __iruid_567 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_567)) (SelectFields (release) (Ref __iruid_567))))) (Let __iruid_568 (ArrayMap __iruid_569 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_569) None (__uid_7 (ApplyIR get Struct{release:Boolean} (Ref __iruid_566) (MakeStruct (s (GetField s (Ref __iruid_569)))))))) (Let __iruid_570 (ArrayMap __iruid_571 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_568)) (I32 1)) (Let __iruid_572 (ArrayRef (Ref __iruid_568) (Ref __iruid_571)) (InsertFields (SelectFields () (Ref __iruid_572)) None (meta (GetField __uid_7 (Ref __iruid_572)))))) (InsertFields (Ref global) ("__cols" "newColIdx") (newColIdx (ArrayFilter __iruid_573 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_570)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_570) (Ref __iruid_573)))) (False))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap __iruid_574 (GetField newColIdx (Ref global)) (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_574)))))) (SelectFields () (Ref global)))) (ArrayAgg __iruid_575 (ArrayFilter __iruid_576 (ArrayRange (I32 0) (ArrayLen (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (I32 1)) (ApplyUnaryPrimOp Bang (IsNA (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_576))))) (MakeStruct (__uid_11 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_575))))))) (I64 0)))))) (Coalesce (GetField __uid_11 (Ref row)) (False)))) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_7_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_7_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_4_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_4_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_4_piece0 on mw-w-0.c.broad-mpg-gnomad.internal:33869 in memory (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_8_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_8_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:25 BlockManagerInfo: INFO: Removed broadcast_8_piece0 on mw-w-0.c.broad-mpg-gnomad.internal:33869 in memory (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:48:25 root: INFO: is/hail/codegen/generated/C_etypeDecode_22. instruction count: 3 2019-10-08 20:48:25 root: INFO: is/hail/codegen/generated/C_etypeDecode_22.apply instruction count: 7 2019-10-08 20:48:25 root: INFO: is/hail/codegen/generated/C_etypeDecode_22.apply instruction count: 12 2019-10-08 20:48:25 root: INFO: is/hail/codegen/generated/C_etypeDecode_22.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23. instruction count: 3 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.apply instruction count: 7 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.apply instruction count: 12 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.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_int32ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_int32ANDo_boolEND_TO_o_tuple_of_o_locusANDo_array_of_o_stringEND_1 instruction count: 155 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_2 instruction count: 22 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_r_binary_TO_r_binary_3 instruction count: 29 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_r_int32_TO_r_int32_4 instruction count: 8 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_array_of_o_binary_TO_o_array_of_o_binary_5 instruction count: 99 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.INPLACE_DECODE_o_binary_TO_o_binary_6 instruction count: 29 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_binary_7 instruction count: 9 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_float64_8 instruction count: 5 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_array_of_o_binary_9 instruction count: 54 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.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_int32ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryEND_10 instruction count: 386 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_array_of_o_int32_11 instruction count: 54 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_int32_12 instruction count: 5 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_array_of_o_float64_13 instruction count: 54 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_23.SKIP_o_bool_14 instruction count: 5 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24. instruction count: 3 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.apply instruction count: 7 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.apply instruction count: 12 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.DECODE_o_struct_of_o_array_of_o_struct_of_o_int32ANDo_binaryANDo_boolENDEND_TO_o_tuple_of_o_array_of_o_tuple_of_o_callANDo_boolENDEND_1 instruction count: 46 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.INPLACE_DECODE_o_array_of_o_struct_of_o_int32ANDo_binaryANDo_boolEND_TO_o_array_of_o_tuple_of_o_int32ANDo_boolEND_2 instruction count: 99 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.INPLACE_DECODE_o_struct_of_o_int32ANDo_binaryANDo_boolEND_TO_o_tuple_of_o_int32ANDo_boolEND_3 instruction count: 79 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.INPLACE_DECODE_o_int32_TO_o_int32_4 instruction count: 8 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.SKIP_o_binary_5 instruction count: 9 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C_etypeDecode_24.INPLACE_DECODE_o_bool_TO_o_bool_6 instruction count: 8 2019-10-08 20:48:26 root: INFO: optimize (Compile): before: IR size 4: (InsertFields (Ref left) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref right)))) 2019-10-08 20:48:26 root: INFO: optimize (Compile): after: IR size 4: (InsertFields (Ref left) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref right)))) 2019-10-08 20:48:26 MemoryStore: INFO: Block broadcast_10 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:48:26 MemoryStore: INFO: Block broadcast_10_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:48:26 BlockManagerInfo: INFO: Added broadcast_10_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:48:26 SparkContext: INFO: Created broadcast 10 from broadcast at SparkBackend.scala:21 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C25. instruction count: 3 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C25.apply instruction count: 142 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C25.apply instruction count: 22 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C25.setPartitionIndex instruction count: 14 2019-10-08 20:48:26 root: INFO: is/hail/codegen/generated/C25.addPartitionRegion instruction count: 6 2019-10-08 20:48:26 root: ERROR: RuntimeException: globals mismatch: typ: Struct{} val: +Struct{} From java.lang.RuntimeException: globals mismatch: typ: Struct{} val: +Struct{} at is.hail.expr.ir.TableValue.(TableValue.scala:50) 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.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableKeyBy.execute(TableIR.scala:366) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableFilter.execute(TableIR.scala:439) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply$mcJ$sp(Interpret.scala:744) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:744) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:744) at scala.Option.getOrElse(Option.scala:121) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:744) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:89) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:59) at is.hail.expr.ir.InterpretNonCompilable$$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:57) at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:57) at is.hail.expr.ir.ExecuteContext$$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:57) at is.hail.backend.Backend.executeJSON(Backend.scala:63) 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) 2019-10-08 20:49:03 ExecutorAllocationManager: INFO: Request to remove executorIds: 2, 1 2019-10-08 20:49:03 YarnClientSchedulerBackend: INFO: Requesting to kill executor(s) 2 2019-10-08 20:49:03 YarnClientSchedulerBackend: INFO: Actual list of executor(s) to be killed is 2 2019-10-08 20:49:03 ExecutorAllocationManager: INFO: Removing executor 2 because it has been idle for 60 seconds (new desired total will be 1) 2019-10-08 20:49:04 YarnSchedulerBackend$YarnDriverEndpoint: INFO: Disabling executor 2. 2019-10-08 20:49:04 DAGScheduler: INFO: Executor lost: 2 (epoch 0) 2019-10-08 20:49:04 BlockManagerMasterEndpoint: INFO: Trying to remove executor 2 from BlockManagerMaster. 2019-10-08 20:49:04 BlockManagerMasterEndpoint: INFO: Removing block manager BlockManagerId(2, mw-w-0.c.broad-mpg-gnomad.internal, 33869, None) 2019-10-08 20:49:04 BlockManagerMaster: INFO: Removed 2 successfully in removeExecutor 2019-10-08 20:49:04 YarnScheduler: INFO: Executor 2 on mw-w-0.c.broad-mpg-gnomad.internal killed by driver. 2019-10-08 20:49:04 ExecutorAllocationManager: INFO: Existing executor 2 has been removed (new total is 1) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 180: (TableCount (MatrixRowsTable (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_13" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_12" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_12 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_14 (GetField __uid_13 (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_14))) (age_hist_het (GetField age_hist_het (Ref __uid_14))) (age_hist_hom (GetField age_hist_hom (Ref __uid_14))) (popmax (GetField popmax (Ref __uid_14))) (faf (GetField faf (Ref __uid_14))) (lcr (GetField lcr (Ref __uid_14))) (decoy (GetField decoy (Ref __uid_14))) (segdup (GetField segdup (Ref __uid_14))) (nonpar (GetField nonpar (Ref __uid_14))) (variant_type (GetField variant_type (Ref __uid_14))) (allele_type (GetField allele_type (Ref __uid_14))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_14))) (was_mixed (GetField was_mixed (Ref __uid_14))) (has_star (GetField has_star (Ref __uid_14))) (qd (GetField qd (Ref __uid_14))) (pab_max (GetField pab_max (Ref __uid_14))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_14))) (info_SOR (GetField info_SOR (Ref __uid_14))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_14))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_14))) (info_FS (GetField info_FS (Ref __uid_14))) (info_QD (GetField info_QD (Ref __uid_14))) (info_MQ (GetField info_MQ (Ref __uid_14))) (info_DP (GetField info_DP (Ref __uid_14))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_14))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_14))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_14))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_14))) (omni (GetField omni (Ref __uid_14))) (mills (GetField mills (Ref __uid_14))) (tp (GetField tp (Ref __uid_14))) (rf_train (GetField rf_train (Ref __uid_14))) (rf_label (GetField rf_label (Ref __uid_14))) (rf_probability (GetField rf_probability (Ref __uid_14))) (rank (GetField rank (Ref __uid_14))) (was_split (GetField was_split (Ref __uid_14))) (singleton (GetField singleton (Ref __uid_14))) (_score (GetField _score (Ref __uid_14))) (_singleton (GetField _singleton (Ref __uid_14))) (biallelic_rank (GetField biallelic_rank (Ref __uid_14))) (singleton_rank (GetField singleton_rank (Ref __uid_14))) (n_nonref (GetField n_nonref (Ref __uid_14))) (score (GetField score (Ref __uid_14))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_14))) (adj_rank (GetField adj_rank (Ref __uid_14))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_14))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_14))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_14))) (filters (GetField filters (Ref __uid_14))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_14))) (gq_hist_all (GetField gq_hist_all (Ref __uid_14))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_14))) (dp_hist_all (GetField dp_hist_all (Ref __uid_14))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_14))) (qual (GetField qual (Ref __uid_14))) (vep (GetField vep (Ref __uid_14))) (allele_info (GetField allele_info (Ref __uid_14))) (rsid (GetField rsid (Ref __uid_14)))))) (Let __uid_15 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_15))) (freq_meta (GetField freq_meta (Ref __uid_15))) (freq_index_dict (GetField freq_index_dict (Ref __uid_15))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_15))) (age_index_dict (GetField age_index_dict (Ref __uid_15))) (faf_index_dict (GetField faf_index_dict (Ref __uid_15))) (age_distribution (GetField age_distribution (Ref __uid_15)))))))) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 1: (I64 290745715) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 1: (I64 290745715) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 1: (I64 290745715) 2019-10-08 20:52:16 root: INFO: optimize (Compile): before: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:52:16 root: INFO: optimize (Compile): after: IR size 2: (MakeTuple (0) (I64 290745715)) 2019-10-08 20:52:16 MemoryStore: INFO: Block broadcast_11 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:52:16 MemoryStore: INFO: Block broadcast_11_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:52:16 BlockManagerInfo: INFO: Added broadcast_11_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:52:16 SparkContext: INFO: Created broadcast 11 from broadcast at SparkBackend.scala:21 2019-10-08 20:52:16 root: INFO: is/hail/codegen/generated/C26. instruction count: 3 2019-10-08 20:52:16 root: INFO: is/hail/codegen/generated/C26.apply instruction count: 53 2019-10-08 20:52:16 root: INFO: is/hail/codegen/generated/C26.apply instruction count: 28 2019-10-08 20:52:16 root: INFO: is/hail/codegen/generated/C26.setPartitionIndex instruction count: 14 2019-10-08 20:52:16 root: INFO: is/hail/codegen/generated/C26.addPartitionRegion instruction count: 6 2019-10-08 20:52:16 root: INFO: Time taken for CompileAndEvaluate -- first pass: 8.535ms 2019-10-08 20:52:16 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 0.236ms 2019-10-08 20:52:16 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 0.106ms 2019-10-08 20:52:16 root: INFO: Time taken for CompileAndEvaluate -- compile: 11.324ms 2019-10-08 20:52:16 root: INFO: Time taken for CompileAndEvaluate -- runtime: 1.161ms 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 180: (TableCount (MatrixColsTable (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_13" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_12" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_12 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_14 (GetField __uid_13 (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_14))) (age_hist_het (GetField age_hist_het (Ref __uid_14))) (age_hist_hom (GetField age_hist_hom (Ref __uid_14))) (popmax (GetField popmax (Ref __uid_14))) (faf (GetField faf (Ref __uid_14))) (lcr (GetField lcr (Ref __uid_14))) (decoy (GetField decoy (Ref __uid_14))) (segdup (GetField segdup (Ref __uid_14))) (nonpar (GetField nonpar (Ref __uid_14))) (variant_type (GetField variant_type (Ref __uid_14))) (allele_type (GetField allele_type (Ref __uid_14))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_14))) (was_mixed (GetField was_mixed (Ref __uid_14))) (has_star (GetField has_star (Ref __uid_14))) (qd (GetField qd (Ref __uid_14))) (pab_max (GetField pab_max (Ref __uid_14))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_14))) (info_SOR (GetField info_SOR (Ref __uid_14))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_14))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_14))) (info_FS (GetField info_FS (Ref __uid_14))) (info_QD (GetField info_QD (Ref __uid_14))) (info_MQ (GetField info_MQ (Ref __uid_14))) (info_DP (GetField info_DP (Ref __uid_14))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_14))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_14))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_14))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_14))) (omni (GetField omni (Ref __uid_14))) (mills (GetField mills (Ref __uid_14))) (tp (GetField tp (Ref __uid_14))) (rf_train (GetField rf_train (Ref __uid_14))) (rf_label (GetField rf_label (Ref __uid_14))) (rf_probability (GetField rf_probability (Ref __uid_14))) (rank (GetField rank (Ref __uid_14))) (was_split (GetField was_split (Ref __uid_14))) (singleton (GetField singleton (Ref __uid_14))) (_score (GetField _score (Ref __uid_14))) (_singleton (GetField _singleton (Ref __uid_14))) (biallelic_rank (GetField biallelic_rank (Ref __uid_14))) (singleton_rank (GetField singleton_rank (Ref __uid_14))) (n_nonref (GetField n_nonref (Ref __uid_14))) (score (GetField score (Ref __uid_14))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_14))) (adj_rank (GetField adj_rank (Ref __uid_14))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_14))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_14))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_14))) (filters (GetField filters (Ref __uid_14))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_14))) (gq_hist_all (GetField gq_hist_all (Ref __uid_14))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_14))) (dp_hist_all (GetField dp_hist_all (Ref __uid_14))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_14))) (qual (GetField qual (Ref __uid_14))) (vep (GetField vep (Ref __uid_14))) (allele_info (GetField allele_info (Ref __uid_14))) (rsid (GetField rsid (Ref __uid_14)))))) (Let __uid_15 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_15))) (freq_meta (GetField freq_meta (Ref __uid_15))) (freq_index_dict (GetField freq_index_dict (Ref __uid_15))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_15))) (age_index_dict (GetField age_index_dict (Ref __uid_15))) (faf_index_dict (GetField faf_index_dict (Ref __uid_15))) (age_distribution (GetField age_distribution (Ref __uid_15)))))))) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 25: (TableCount (MatrixColsTable (MatrixFilterCols (MatrixMapCols () (MatrixAnnotateColsTable "__uid_12" (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/genomes/gnomad.genomes.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/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_12 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))))) 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 155: (TableCount (TableKeyBy () False (TableParallelize None (Let __cols_and_globals (TableGetGlobals (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/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (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_595 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_595)) (SelectFields (release) (Ref __iruid_595))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_594 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_594) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_594)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_599 (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_599)) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_12 (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)))))))) (MakeStruct (rows (GetField __cols (Ref __cols_and_globals))) (global (SelectFields () (Ref __cols_and_globals)))))))) 2019-10-08 20:52:16 root: INFO: Prune: MakeStruct: eliminating field 'global' 2019-10-08 20:52:16 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 61: (Cast Int64 (ArrayLen (GetField rows (Let __iruid_713 (ToDict (ArrayMap __iruid_714 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_714)) (SelectFields (release) (Ref __iruid_714))))) (Let __iruid_715 (ArrayMap __iruid_716 (GetField rows (TableCollect (TableRead Table{global:Struct{},key:[],row:Struct{s:String}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}"))) (InsertFields (Ref __iruid_716) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __iruid_713) (MakeStruct (s (GetField s (Ref __iruid_716)))))))) (Let __iruid_717 (ArrayMap __iruid_718 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_715)) (I32 1)) (Let __iruid_719 (ArrayRef (Ref __iruid_715) (Ref __iruid_718)) (InsertFields (SelectFields () (Ref __iruid_719)) None (meta (GetField __uid_12 (Ref __iruid_719)))))) (MakeStruct (rows (ArrayMap __iruid_720 (ArrayFilter __iruid_721 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_717)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_717) (Ref __iruid_721)))) (False))) (ArrayRef (Ref __iruid_717) (Ref __iruid_720))))))))))) 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_27. instruction count: 3 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_27.apply instruction count: 7 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_27.apply instruction count: 12 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_27.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_28. instruction count: 3 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_28.apply instruction count: 7 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_28.apply instruction count: 12 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_28.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_28.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeEncode_29. instruction count: 3 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeEncode_29.apply instruction count: 7 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeEncode_29.apply instruction count: 11 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeEncode_29.ENCODE_o_tuple_of_o_stringEND_TO_o_struct_of_o_binaryEND_1 instruction count: 25 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeEncode_29.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:52:17 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:52:17 DAGScheduler: INFO: Got job 4 (collect at RVD.scala:685) with 1 output partitions 2019-10-08 20:52:17 DAGScheduler: INFO: Final stage: ResultStage 4 (collect at RVD.scala:685) 2019-10-08 20:52:17 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:52:17 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:52:17 DAGScheduler: INFO: Submitting ResultStage 4 (MapPartitionsRDD[32] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:52:17 MemoryStore: INFO: Block broadcast_12 stored as values in memory (estimated size 10.5 KB, free 21.7 GB) 2019-10-08 20:52:17 MemoryStore: INFO: Block broadcast_12_piece0 stored as bytes in memory (estimated size 5.7 KB, free 21.7 GB) 2019-10-08 20:52:17 BlockManagerInfo: INFO: Added broadcast_12_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:52:17 SparkContext: INFO: Created broadcast 12 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:52:17 DAGScheduler: INFO: Submitting 1 missing tasks from ResultStage 4 (MapPartitionsRDD[32] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0)) 2019-10-08 20:52:17 YarnScheduler: INFO: Adding task set 4.0 with 1 tasks 2019-10-08 20:52:17 FairSchedulableBuilder: INFO: Added task set TaskSet_4.0 tasks to pool default 2019-10-08 20:52:17 TaskSetManager: INFO: Starting task 0.0 in stage 4.0 (TID 22, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7664 bytes) 2019-10-08 20:52:17 BlockManagerInfo: INFO: Added broadcast_12_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:52:17 TaskSetManager: INFO: Finished task 0.0 in stage 4.0 (TID 22) in 415 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/1) 2019-10-08 20:52:17 YarnScheduler: INFO: Removed TaskSet 4.0, whose tasks have all completed, from pool default 2019-10-08 20:52:17 DAGScheduler: INFO: ResultStage 4 (collect at RVD.scala:685) finished in 0.425 s 2019-10-08 20:52:17 DAGScheduler: INFO: Job 4 finished: collect at RVD.scala:685, took 0.428655 s 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_30. instruction count: 3 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_30.apply instruction count: 7 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_30.apply instruction count: 12 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_30.DECODE_o_struct_of_o_binaryEND_TO_o_tuple_of_o_stringEND_1 instruction count: 46 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_30.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_31. instruction count: 3 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_31.apply instruction count: 7 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_31.apply instruction count: 12 2019-10-08 20:52:17 root: INFO: is/hail/codegen/generated/C_etypeDecode_31.DECODE_o_struct_of_END_TO_o_tuple_of_END_1 instruction count: 14 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32. instruction count: 3 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.apply instruction count: 7 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.apply instruction count: 12 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.DECODE_o_struct_of_o_binaryANDo_float64ANDo_float64ANDo_boolANDo_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int32ANDo_float64ANDo_boolANDo_boolANDo_binaryANDo_boolANDo_binaryANDo_binaryANDo_binaryANDo_binaryANDo_int32ANDo_binaryANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_boolANDo_binaryANDo_boolANDo_float64ANDo_boolANDo_boolANDo_array_of_o_binaryANDo_array_of_o_binaryANDo_binaryANDo_binaryANDo_binaryANDo_boolANDo_binaryANDo_int32ANDo_binaryANDo_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDENDANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_boolANDo_array_of_o_binaryANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryANDo_binaryANDo_boolANDo_boolANDo_binaryANDo_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 979 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_float64_3 instruction count: 5 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_bool_4 instruction count: 5 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_binary_5 instruction count: 9 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_int32_6 instruction count: 5 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_array_of_o_binary_7 instruction count: 54 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_struct_of_o_float64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_int64ANDo_float64ANDo_float64ANDo_float64ANDo_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64ENDEND_8 instruction count: 337 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_int64_9 instruction count: 5 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.SKIP_o_struct_of_o_float64ANDo_int64ANDo_float64ANDo_int64END_10 instruction count: 71 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_32.INPLACE_DECODE_o_bool_TO_o_bool_11 instruction count: 8 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33. instruction count: 3 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33.apply instruction count: 7 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33.apply instruction count: 11 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33.ENCODE_o_tuple_of_o_stringANDo_boolEND_TO_o_struct_of_o_binaryANDo_boolEND_1 instruction count: 43 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33.ENCODE_o_binary_TO_o_binary_2 instruction count: 16 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeEncode_33.ENCODE_o_bool_TO_o_bool_3 instruction count: 6 2019-10-08 20:52:18 SparkContext: INFO: Starting job: collect at RVD.scala:685 2019-10-08 20:52:18 DAGScheduler: INFO: Got job 5 (collect at RVD.scala:685) with 10 output partitions 2019-10-08 20:52:18 DAGScheduler: INFO: Final stage: ResultStage 5 (collect at RVD.scala:685) 2019-10-08 20:52:18 DAGScheduler: INFO: Parents of final stage: List() 2019-10-08 20:52:18 DAGScheduler: INFO: Missing parents: List() 2019-10-08 20:52:18 DAGScheduler: INFO: Submitting ResultStage 5 (MapPartitionsRDD[38] at mapPartitions at ContextRDD.scala:216), which has no missing parents 2019-10-08 20:52:18 MemoryStore: INFO: Block broadcast_13 stored as values in memory (estimated size 26.7 KB, free 21.7 GB) 2019-10-08 20:52:18 MemoryStore: INFO: Block broadcast_13_piece0 stored as bytes in memory (estimated size 13.1 KB, free 21.7 GB) 2019-10-08 20:52:18 BlockManagerInfo: INFO: Added broadcast_13_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:52:18 SparkContext: INFO: Created broadcast 13 from broadcast at DAGScheduler.scala:1161 2019-10-08 20:52:18 DAGScheduler: INFO: Submitting 10 missing tasks from ResultStage 5 (MapPartitionsRDD[38] at mapPartitions at ContextRDD.scala:216) (first 15 tasks are for partitions Vector(0, 1, 2, 3, 4, 5, 6, 7, 8, 9)) 2019-10-08 20:52:18 YarnScheduler: INFO: Adding task set 5.0 with 10 tasks 2019-10-08 20:52:18 FairSchedulableBuilder: INFO: Added task set TaskSet_5.0 tasks to pool default 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 0.0 in stage 5.0 (TID 23, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 0, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 1.0 in stage 5.0 (TID 24, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 1, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 2.0 in stage 5.0 (TID 25, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 2, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 3.0 in stage 5.0 (TID 26, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 3, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 BlockManagerInfo: INFO: Added broadcast_13_piece0 in memory on mw-w-1.c.broad-mpg-gnomad.internal:42975 (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 4.0 in stage 5.0 (TID 27, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 4, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 1.0 in stage 5.0 (TID 24) in 202 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (1/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 5.0 in stage 5.0 (TID 28, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 5, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 2.0 in stage 5.0 (TID 25) in 221 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (2/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 6.0 in stage 5.0 (TID 29, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 6, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 3.0 in stage 5.0 (TID 26) in 239 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (3/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 7.0 in stage 5.0 (TID 30, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 7, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 0.0 in stage 5.0 (TID 23) in 251 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (4/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 8.0 in stage 5.0 (TID 31, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 8, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 5.0 in stage 5.0 (TID 28) in 107 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (5/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Starting task 9.0 in stage 5.0 (TID 32, mw-w-1.c.broad-mpg-gnomad.internal, executor 1, partition 9, PROCESS_LOCAL, 7709 bytes) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 7.0 in stage 5.0 (TID 30) in 123 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (6/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 4.0 in stage 5.0 (TID 27) in 186 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (7/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 6.0 in stage 5.0 (TID 29) in 164 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (8/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 8.0 in stage 5.0 (TID 31) in 96 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (9/10) 2019-10-08 20:52:18 TaskSetManager: INFO: Finished task 9.0 in stage 5.0 (TID 32) in 93 ms on mw-w-1.c.broad-mpg-gnomad.internal (executor 1) (10/10) 2019-10-08 20:52:18 YarnScheduler: INFO: Removed TaskSet 5.0, whose tasks have all completed, from pool default 2019-10-08 20:52:18 DAGScheduler: INFO: ResultStage 5 (collect at RVD.scala:685) finished in 0.473 s 2019-10-08 20:52:18 DAGScheduler: INFO: Job 5 finished: collect at RVD.scala:685, took 0.478640 s 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34. instruction count: 3 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34.apply instruction count: 7 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34.apply instruction count: 12 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34.DECODE_o_struct_of_o_binaryANDo_boolEND_TO_o_tuple_of_o_stringANDo_boolEND_1 instruction count: 71 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34.INPLACE_DECODE_o_binary_TO_o_binary_2 instruction count: 29 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C_etypeDecode_34.INPLACE_DECODE_o_bool_TO_o_bool_3 instruction count: 8 2019-10-08 20:52:18 root: INFO: optimize (Compile): before: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_713 (ToDict (ArrayMap __iruid_714 (GetField rows (GetField __iruid_733 (Ref __iruid_731))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_714)) (SelectFields (release) (Ref __iruid_714))))) (Let __iruid_715 (ArrayMap __iruid_716 (GetField rows (GetField __iruid_732 (Ref __iruid_731))) (InsertFields (Ref __iruid_716) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __iruid_713) (MakeStruct (s (GetField s (Ref __iruid_716)))))))) (Let __iruid_717 (ArrayMap __iruid_718 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_715)) (I32 1)) (Let __iruid_719 (ArrayRef (Ref __iruid_715) (Ref __iruid_718)) (InsertFields (SelectFields () (Ref __iruid_719)) None (meta (GetField __uid_12 (Ref __iruid_719)))))) (MakeStruct (rows (ArrayMap __iruid_720 (ArrayFilter __iruid_721 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_717)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_717) (Ref __iruid_721)))) (False))) (ArrayRef (Ref __iruid_717) (Ref __iruid_720)))))))))))) 2019-10-08 20:52:18 root: INFO: optimize (Compile): after: IR size 61: (MakeTuple (0) (Cast Int64 (ArrayLen (GetField rows (Let __iruid_784 (ToDict (ArrayMap __iruid_785 (GetField rows (GetField __iruid_733 (Ref __iruid_731))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_785)) (SelectFields (release) (Ref __iruid_785))))) (Let __iruid_786 (ArrayMap __iruid_787 (GetField rows (GetField __iruid_732 (Ref __iruid_731))) (InsertFields (Ref __iruid_787) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __iruid_784) (MakeStruct (s (GetField s (Ref __iruid_787)))))))) (Let __iruid_788 (ArrayMap __iruid_789 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_786)) (I32 1)) (Let __iruid_790 (ArrayRef (Ref __iruid_786) (Ref __iruid_789)) (InsertFields (SelectFields () (Ref __iruid_790)) None (meta (GetField __uid_12 (Ref __iruid_790)))))) (MakeStruct (rows (ArrayMap __iruid_791 (ArrayFilter __iruid_792 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_788)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_788) (Ref __iruid_792)))) (False))) (ArrayRef (Ref __iruid_788) (Ref __iruid_791)))))))))))) 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36. instruction count: 3 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.apply instruction count: 11 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.apply instruction count: 14 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.method_1 instruction count: 110 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.method_2 instruction count: 45 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.method_3 instruction count: 92 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C36.method_4 instruction count: 105 2019-10-08 20:52:18 MemoryStore: INFO: Block broadcast_14 stored as values in memory (estimated size 56.0 B, free 21.7 GB) 2019-10-08 20:52:18 MemoryStore: INFO: Block broadcast_14_piece0 stored as bytes in memory (estimated size 45.0 B, free 21.7 GB) 2019-10-08 20:52:18 BlockManagerInfo: INFO: Added broadcast_14_piece0 in memory on mw-m.c.broad-mpg-gnomad.internal:43029 (size: 45.0 B, free: 21.7 GB) 2019-10-08 20:52:18 SparkContext: INFO: Created broadcast 14 from broadcast at SparkBackend.scala:21 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35. instruction count: 3 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.apply instruction count: 45 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.apply instruction count: 28 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_1 instruction count: 1890 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_2 instruction count: 99 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_3 instruction count: 83 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_4 instruction count: 106 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_5 instruction count: 64 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_6 instruction count: 563 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_7 instruction count: 87 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_8 instruction count: 92 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_9 instruction count: 105 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_10 instruction count: 37 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.method_11 instruction count: 725 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.setPartitionIndex instruction count: 14 2019-10-08 20:52:18 root: INFO: is/hail/codegen/generated/C35.addPartitionRegion instruction count: 6 2019-10-08 20:52:18 root: INFO: Time taken for CompileAndEvaluate -- first pass: 22.782ms 2019-10-08 20:52:18 root: INFO: Time taken for CompileAndEvaluate -- after Matrix lowering: 77.544ms 2019-10-08 20:52:18 root: INFO: Time taken for CompileAndEvaluate -- interpret non-compilable: 1.662s 2019-10-08 20:52:18 root: INFO: Time taken for CompileAndEvaluate -- compile: 44.462ms 2019-10-08 20:52:18 root: INFO: Time taken for CompileAndEvaluate -- runtime: 111.466ms 2019-10-08 20:52:18 root: INFO: optimize (CompileAndEvaluate: first pass): before: IR size 441: (TableCount (MatrixRowsTable (MatrixMapRows (MatrixFilterRows (MatrixMapRows (MatrixMapGlobals (MatrixMapRows (MatrixAnnotateRowsTable "__uid_13" False (MatrixFilterCols (MatrixMapCols None (MatrixAnnotateColsTable "__uid_12" (MatrixMapEntries (MatrixFilterEntries (MatrixRead None False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.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/genomes/gnomad.genomes.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 pcr_free project_name release_2_0_2) (SelectFields (s callrate mean_dp pcr_free product_simplified freemix pct_chimeras mean_read_length pct_reads_aligned_in_pairs median_insert_size mean_insert_size release_2_0_2 neuro project_id releasable_2_0_2 product investigator project_description project_name gvcf_date bam gvcf control age releasable_2_1 internal cloudable qc_platform syndip f_stat is_female ambiguous_sex hard_filters perm_filters sex data_type 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 fail_call_rate 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_12 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False))) (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (Let __uid_14 (GetField __uid_13 (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_14))) (age_hist_het (GetField age_hist_het (Ref __uid_14))) (age_hist_hom (GetField age_hist_hom (Ref __uid_14))) (popmax (GetField popmax (Ref __uid_14))) (faf (GetField faf (Ref __uid_14))) (lcr (GetField lcr (Ref __uid_14))) (decoy (GetField decoy (Ref __uid_14))) (segdup (GetField segdup (Ref __uid_14))) (nonpar (GetField nonpar (Ref __uid_14))) (variant_type (GetField variant_type (Ref __uid_14))) (allele_type (GetField allele_type (Ref __uid_14))) (n_alt_alleles (GetField n_alt_alleles (Ref __uid_14))) (was_mixed (GetField was_mixed (Ref __uid_14))) (has_star (GetField has_star (Ref __uid_14))) (qd (GetField qd (Ref __uid_14))) (pab_max (GetField pab_max (Ref __uid_14))) (info_MQRankSum (GetField info_MQRankSum (Ref __uid_14))) (info_SOR (GetField info_SOR (Ref __uid_14))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref __uid_14))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref __uid_14))) (info_FS (GetField info_FS (Ref __uid_14))) (info_QD (GetField info_QD (Ref __uid_14))) (info_MQ (GetField info_MQ (Ref __uid_14))) (info_DP (GetField info_DP (Ref __uid_14))) (transmitted_singleton (GetField transmitted_singleton (Ref __uid_14))) (fail_hard_filters (GetField fail_hard_filters (Ref __uid_14))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref __uid_14))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref __uid_14))) (omni (GetField omni (Ref __uid_14))) (mills (GetField mills (Ref __uid_14))) (tp (GetField tp (Ref __uid_14))) (rf_train (GetField rf_train (Ref __uid_14))) (rf_label (GetField rf_label (Ref __uid_14))) (rf_probability (GetField rf_probability (Ref __uid_14))) (rank (GetField rank (Ref __uid_14))) (was_split (GetField was_split (Ref __uid_14))) (singleton (GetField singleton (Ref __uid_14))) (_score (GetField _score (Ref __uid_14))) (_singleton (GetField _singleton (Ref __uid_14))) (biallelic_rank (GetField biallelic_rank (Ref __uid_14))) (singleton_rank (GetField singleton_rank (Ref __uid_14))) (n_nonref (GetField n_nonref (Ref __uid_14))) (score (GetField score (Ref __uid_14))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref __uid_14))) (adj_rank (GetField adj_rank (Ref __uid_14))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref __uid_14))) (adj_singleton_rank (GetField adj_singleton_rank (Ref __uid_14))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref __uid_14))) (filters (GetField filters (Ref __uid_14))) (gq_hist_alt (GetField gq_hist_alt (Ref __uid_14))) (gq_hist_all (GetField gq_hist_all (Ref __uid_14))) (dp_hist_alt (GetField dp_hist_alt (Ref __uid_14))) (dp_hist_all (GetField dp_hist_all (Ref __uid_14))) (ab_hist_alt (GetField ab_hist_alt (Ref __uid_14))) (qual (GetField qual (Ref __uid_14))) (vep (GetField vep (Ref __uid_14))) (allele_info (GetField allele_info (Ref __uid_14))) (rsid (GetField rsid (Ref __uid_14)))))) (Let __uid_15 (TableGetGlobals (TableRead None False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad-public/release/2.1.1/ht/genomes/gnomad.genomes.r2.1.1.sites.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (SelectFields () (Ref global))) None (rf (GetField rf (Ref __uid_15))) (freq_meta (GetField freq_meta (Ref __uid_15))) (freq_index_dict (GetField freq_index_dict (Ref __uid_15))) (popmax_index_dict (GetField popmax_index_dict (Ref __uid_15))) (age_index_dict (GetField age_index_dict (Ref __uid_15))) (faf_index_dict (GetField faf_index_dict (Ref __uid_15))) (age_distribution (GetField age_distribution (Ref __uid_15)))))) (InsertFields (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (freq (GetField freq (Ref va))) (age_hist_het (GetField age_hist_het (Ref va))) (age_hist_hom (GetField age_hist_hom (Ref va))) (popmax (GetField popmax (Ref va))) (faf (GetField faf (Ref va))) (lcr (GetField lcr (Ref va))) (decoy (GetField decoy (Ref va))) (segdup (GetField segdup (Ref va))) (nonpar (GetField nonpar (Ref va))) (variant_type (GetField variant_type (Ref va))) (allele_type (GetField allele_type (Ref va))) (n_alt_alleles (GetField n_alt_alleles (Ref va))) (was_mixed (GetField was_mixed (Ref va))) (has_star (GetField has_star (Ref va))) (qd (GetField qd (Ref va))) (pab_max (GetField pab_max (Ref va))) (info_MQRankSum (GetField info_MQRankSum (Ref va))) (info_SOR (GetField info_SOR (Ref va))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref va))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref va))) (info_FS (GetField info_FS (Ref va))) (info_QD (GetField info_QD (Ref va))) (info_MQ (GetField info_MQ (Ref va))) (info_DP (GetField info_DP (Ref va))) (transmitted_singleton (GetField transmitted_singleton (Ref va))) (fail_hard_filters (GetField fail_hard_filters (Ref va))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref va))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref va))) (omni (GetField omni (Ref va))) (mills (GetField mills (Ref va))) (tp (GetField tp (Ref va))) (rf_train (GetField rf_train (Ref va))) (rf_label (GetField rf_label (Ref va))) (rf_probability (GetField rf_probability (Ref va))) (rank (GetField rank (Ref va))) (was_split (GetField was_split (Ref va))) (singleton (GetField singleton (Ref va))) (_score (GetField _score (Ref va))) (_singleton (GetField _singleton (Ref va))) (biallelic_rank (GetField biallelic_rank (Ref va))) (singleton_rank (GetField singleton_rank (Ref va))) (n_nonref (GetField n_nonref (Ref va))) (score (GetField score (Ref va))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref va))) (adj_rank (GetField adj_rank (Ref va))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref va))) (adj_singleton_rank (GetField adj_singleton_rank (Ref va))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref va))) (filters (GetField filters (Ref va))) (gq_hist_alt (GetField gq_hist_alt (Ref va))) (gq_hist_all (GetField gq_hist_all (Ref va))) (dp_hist_alt (GetField dp_hist_alt (Ref va))) (dp_hist_all (GetField dp_hist_all (Ref va))) (ab_hist_alt (GetField ab_hist_alt (Ref va))) (qual (GetField qual (Ref va))) (vep (GetField vep (Ref va))) (allele_info (GetField allele_info (Ref va))) (rsid (GetField rsid (Ref va)))) None (__uid_16 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (ApplyIR toInt64 Int64 (I32 0)))))) (Coalesce (GetField __uid_16 (Ref va)) (False))) (SelectFields (locus alleles freq age_hist_het age_hist_hom popmax faf lcr decoy segdup nonpar variant_type allele_type n_alt_alleles was_mixed has_star qd pab_max info_MQRankSum info_SOR info_InbreedingCoeff info_ReadPosRankSum info_FS info_QD info_MQ info_DP transmitted_singleton fail_hard_filters info_POSITIVE_TRAIN_SITE info_NEGATIVE_TRAIN_SITE omni mills tp rf_train rf_label rf_probability rank was_split singleton _score _singleton biallelic_rank singleton_rank n_nonref score adj_biallelic_singleton_rank adj_rank adj_biallelic_rank adj_singleton_rank biallelic_singleton_rank filters gq_hist_alt gq_hist_all dp_hist_alt dp_hist_all ab_hist_alt qual vep allele_info rsid) (MakeStruct (locus (GetField locus (Ref va))) (alleles (GetField alleles (Ref va))) (freq (GetField freq (Ref va))) (age_hist_het (GetField age_hist_het (Ref va))) (age_hist_hom (GetField age_hist_hom (Ref va))) (popmax (GetField popmax (Ref va))) (faf (GetField faf (Ref va))) (lcr (GetField lcr (Ref va))) (decoy (GetField decoy (Ref va))) (segdup (GetField segdup (Ref va))) (nonpar (GetField nonpar (Ref va))) (variant_type (GetField variant_type (Ref va))) (allele_type (GetField allele_type (Ref va))) (n_alt_alleles (GetField n_alt_alleles (Ref va))) (was_mixed (GetField was_mixed (Ref va))) (has_star (GetField has_star (Ref va))) (qd (GetField qd (Ref va))) (pab_max (GetField pab_max (Ref va))) (info_MQRankSum (GetField info_MQRankSum (Ref va))) (info_SOR (GetField info_SOR (Ref va))) (info_InbreedingCoeff (GetField info_InbreedingCoeff (Ref va))) (info_ReadPosRankSum (GetField info_ReadPosRankSum (Ref va))) (info_FS (GetField info_FS (Ref va))) (info_QD (GetField info_QD (Ref va))) (info_MQ (GetField info_MQ (Ref va))) (info_DP (GetField info_DP (Ref va))) (transmitted_singleton (GetField transmitted_singleton (Ref va))) (fail_hard_filters (GetField fail_hard_filters (Ref va))) (info_POSITIVE_TRAIN_SITE (GetField info_POSITIVE_TRAIN_SITE (Ref va))) (info_NEGATIVE_TRAIN_SITE (GetField info_NEGATIVE_TRAIN_SITE (Ref va))) (omni (GetField omni (Ref va))) (mills (GetField mills (Ref va))) (tp (GetField tp (Ref va))) (rf_train (GetField rf_train (Ref va))) (rf_label (GetField rf_label (Ref va))) (rf_probability (GetField rf_probability (Ref va))) (rank (GetField rank (Ref va))) (was_split (GetField was_split (Ref va))) (singleton (GetField singleton (Ref va))) (_score (GetField _score (Ref va))) (_singleton (GetField _singleton (Ref va))) (biallelic_rank (GetField biallelic_rank (Ref va))) (singleton_rank (GetField singleton_rank (Ref va))) (n_nonref (GetField n_nonref (Ref va))) (score (GetField score (Ref va))) (adj_biallelic_singleton_rank (GetField adj_biallelic_singleton_rank (Ref va))) (adj_rank (GetField adj_rank (Ref va))) (adj_biallelic_rank (GetField adj_biallelic_rank (Ref va))) (adj_singleton_rank (GetField adj_singleton_rank (Ref va))) (biallelic_singleton_rank (GetField biallelic_singleton_rank (Ref va))) (filters (GetField filters (Ref va))) (gq_hist_alt (GetField gq_hist_alt (Ref va))) (gq_hist_all (GetField gq_hist_all (Ref va))) (dp_hist_alt (GetField dp_hist_alt (Ref va))) (dp_hist_all (GetField dp_hist_all (Ref va))) (ab_hist_alt (GetField ab_hist_alt (Ref va))) (qual (GetField qual (Ref va))) (vep (GetField vep (Ref va))) (allele_info (GetField allele_info (Ref va))) (rsid (GetField rsid (Ref va))) (__uid_16 (GetField __uid_16 (Ref va)))))))) 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'freq' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'age_hist_het' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'age_hist_hom' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'popmax' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'faf' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'lcr' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'decoy' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'segdup' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'nonpar' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'variant_type' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'allele_type' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'n_alt_alleles' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'was_mixed' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'has_star' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'qd' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'pab_max' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_MQRankSum' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_SOR' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_FS' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_QD' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_MQ' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_DP' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'transmitted_singleton' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'fail_hard_filters' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'omni' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'mills' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'tp' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rf_train' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rf_label' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rf_probability' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'was_split' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'singleton' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field '_score' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field '_singleton' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'n_nonref' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'score' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'adj_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'adj_biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'adj_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'filters' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'gq_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'dp_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'ab_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'qual' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'vep' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'allele_info' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rsid' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'rf' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'freq_meta' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'freq_index_dict' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'popmax_index_dict' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'age_index_dict' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'faf_index_dict' 2019-10-08 20:52:18 root: INFO: Prune: InsertFields: eliminating field 'age_distribution' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'freq' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_het' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_hom' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'popmax' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'faf' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'lcr' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'decoy' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'segdup' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'nonpar' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'variant_type' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'allele_type' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'n_alt_alleles' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'was_mixed' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'has_star' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'qd' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'pab_max' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_MQRankSum' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_SOR' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_FS' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_QD' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_MQ' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_DP' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'transmitted_singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'fail_hard_filters' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'omni' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'mills' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'tp' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_train' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_label' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_probability' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'was_split' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field '_score' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field '_singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'n_nonref' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'score' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'filters' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'ab_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'qual' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'vep' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'allele_info' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rsid' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'locus' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'alleles' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'freq' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_het' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'age_hist_hom' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'popmax' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'faf' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'lcr' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'decoy' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'segdup' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'nonpar' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'variant_type' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'allele_type' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'n_alt_alleles' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'was_mixed' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'has_star' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'qd' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'pab_max' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_MQRankSum' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_SOR' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_InbreedingCoeff' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_ReadPosRankSum' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_FS' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_QD' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_MQ' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_DP' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'transmitted_singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'fail_hard_filters' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_POSITIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'info_NEGATIVE_TRAIN_SITE' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'omni' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'mills' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'tp' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_train' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_label' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rf_probability' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'was_split' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field '_score' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field '_singleton' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'n_nonref' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'score' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_biallelic_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'adj_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'biallelic_singleton_rank' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'filters' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'gq_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'dp_hist_all' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'ab_hist_alt' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'qual' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'vep' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'allele_info' 2019-10-08 20:52:18 root: INFO: Prune: MakeStruct: eliminating field 'rsid' 2019-10-08 20:52:19 root: INFO: Prune: MakeStruct: eliminating field 'locus' 2019-10-08 20:52:19 root: INFO: Prune: MakeStruct: eliminating field 'alleles' 2019-10-08 20:52:19 root: INFO: optimize (CompileAndEvaluate: first pass): after: IR size 43: (TableCount (MatrixRowsTable (MatrixMapRows (MatrixKeyRowsBy () False (MatrixFilterRows (MatrixMapRows (MatrixKeyRowsBy () False (MatrixFilterCols (MatrixMapCols () (MatrixAnnotateColsTable "__uid_12" (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{GT:Call,adj:Boolean}} False False "{\"name\":\"MatrixNativeReader\",\"path\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt\",\"_spec\":null}") (Coalesce (GetField adj (Ref g)) (False))) (SelectFields (GT) (Ref g))) (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_12 (Ref sa))))) (Coalesce (GetField release (GetField meta (Ref sa))) (False)))) (MakeStruct (__uid_16 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (I64 0))))) (Coalesce (GetField __uid_16 (Ref va)) (False)))) (Literal Struct{} )))) 2019-10-08 20:52:19 BlockManagerInfo: INFO: Removed broadcast_12_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 5.7 KB, free: 21.7 GB) 2019-10-08 20:52:19 BlockManagerInfo: INFO: Removed broadcast_12_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 5.7 KB, free: 9.5 GB) 2019-10-08 20:52:19 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): before: IR size 201: (TableCount (TableMapRows (TableMapGlobals (TableMapRows (TableKeyBy () False (TableFilter (TableMapRows (TableKeyBy () False (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{GT:Call,adj:Boolean}]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (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{GT:Call,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 (GT) (Ref g)))))))) (Let __dictfield (ToDict (ArrayMap __iruid_811 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_811)) (SelectFields (release) (Ref __iruid_811))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_810 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_810) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __dictfield) (MakeStruct (s (GetField s (Ref __iruid_810)))))))))))) (InsertFields (Ref global) None (__cols (ArrayMap __iruid_815 (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_815)) (InsertFields (SelectFields () (Ref sa)) None (meta (GetField __uid_12 (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)))))))) (InsertFields (ArrayAgg i (ArrayFilter i (ArrayRange (I32 0) (ArrayLen (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (I32 1)) (ApplyUnaryPrimOp Bang (IsNA (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i))))) (AggLet sa False (ArrayRef (GetField __cols (Ref global)) (Ref i)) (AggLet g False (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref i)) (MakeStruct (__uid_16 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (Ref g)))))) (I64 0))))))) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))))) (Coalesce (GetField __uid_16 (SelectFields (__uid_16) (Ref row))) (False)))) (InsertFields (Literal Struct{} ) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))))) (SelectFields () (Ref global))) (SelectFields () (Ref row)))) 2019-10-08 20:52:19 BlockManagerInfo: INFO: Removed broadcast_13_piece0 on mw-m.c.broad-mpg-gnomad.internal:43029 in memory (size: 13.1 KB, free: 21.7 GB) 2019-10-08 20:52:19 BlockManagerInfo: INFO: Removed broadcast_13_piece0 on mw-w-1.c.broad-mpg-gnomad.internal:42975 in memory (size: 13.1 KB, free: 9.5 GB) 2019-10-08 20:52:19 root: INFO: Prune: InsertFields: eliminating field '__cols' 2019-10-08 20:52:19 root: INFO: Prune: InsertFields: eliminating field '__cols' 2019-10-08 20:52:19 root: INFO: Prune: InsertFields: eliminating field 'the entries! [877f12a8827e18f61222c6c8c5fb04a8]' 2019-10-08 20:52:19 root: INFO: optimize (CompileAndEvaluate: after Matrix lowering): after: IR size 142: (TableCount (TableFilter (TableMapRows (TableKeyBy () False (TableMapGlobals (TableMapRows (TableMapGlobals (TableMapRows (TableMapGlobals (TableRead Table{global:Struct{},key:[locus,alleles],row:Struct{locus:Locus(GRCh37),alleles:Array[String],`the entries! [877f12a8827e18f61222c6c8c5fb04a8]`:Array[Struct{GT:Call,adj:Boolean}]}} False "{\"name\":\"TableNativeZippedReader\",\"pathLeft\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/rows\",\"pathRight\":\"gs://gnomad/hardcalls/hail-0.2/mt/genomes/gnomad.genomes.mt/entries\",\"_specLeft\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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,MQ0:Int32,MQRankSum:Float64,NEGATIVE_TRAIN_SITE:Boolean,POSITIVE_TRAIN_SITE:Boolean,QD:Float64,RAW_MQ: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\":[40898,33984,33886,34874,34984,35210,21024,35211,34983,31587,33191,34585,26997,34099,34626,34968,30772,35184,35795,35336,34388,26453,34943,35454,35724,35754,32155,35505,35778,36236,35830,26829,35384,35957,36055,35712,35776,23058,35717,35226,35264,36081,24837,34734,43172,35563,35479,20980,36160,35248,35214,35325,22970,35099,35549,41880,35157,26054,35135,35690,35816,36607,35440,35766,35369,35648,31767,35479,35697,35942,35629,20708,35570,35252,35211,34269,35842,35873,37536,24527,36236,35711,36975,35680,31980,35521,36226,36121,35896,35893,36122,35831,36446,35865,35602,35359,25376,35408,35969,35555,32446,36245,36197,36099,35937,36036,35999,27107,36405,35681,36456,36495,36561,22739,35585,35495,35836,35770,25466,35856,36048,35596,36167,37116,35878,36113,35730,36136,31570,35939,36348,35914,35920,32636,35629,35451,36091,36207,36019,26065,35965,36018,35586,36541,27780,35924,35993,36182,36192,36761,24688,37097,36309,36742,36501,36540,36523,36459,36061,29720,35143,35344,35975,35660,24632,35317,36089,35951,26738,36251,36018,36323,35944,36176,36589,35791,20293,36166,36609,36690,36525,36441,33796,36193,35847,35262,20657,36364,36304,36230,34643,35658,36428,36133,36333,21914,36531,36227,36567,31143,35936,36227,35932,38084,36824,36555,36573,36701,24270,36215,36574,36849,36766,31198,36413,36155,36236,27928,36706,36690,36342,36313,21831,35980,35989,36177,31282,36332,36207,36298,36291,27308,36163,36289,35988,28094,36317,36292,36578,36187,22598,36455,36525,36096,22597,36741,35949,36608,36100,28879,36023,36770,36280,21932,36480,36248,36189,36479,37330,36261,36069,36375,24565,36647,36404,36318,36129,33428,35904,36289,36398,29993,36293,36110,36188,32239,35917,36162,36195,36274,21019,36274,36555,36311,36806,23615,36384,36161,36323,36237,33551,36131,36394,36439,36081,20187,36180,36222,21452,36465,36400,37390,36395,19761,35878,36794,25699,36025,36872,36612,36390,23000,36352,36214,36304,26439,37198,35849,35969,36505,33695,35808,36017,35810,36187,36045,36184,35884,35939,36560,36152,35877,36345,36170,30125,35832,36223,36497,36196,23515,36165,36255,36557,32770,21696,20958,21578,24098,20858,25144,21795,31506,23273,43155,25744,23785,37620,20380,27662,34062,30489,11971,23630,24835,46021,23370,25256,24697,22379,28258,26166,21218,30526,34685,23526,28453,40823,22331,35878,32341,23114,31956,35560,35808,35778,35974,28697,35750,36147,36102,35779,23975,35703,36086,35635,35619,36005,21897,36033,35734,36010,35853,34126,36057,36080,36066,22744,36056,36441,36479,34371,35982,35813,35622,35841,33512,36070,35891,36453,26612,36073,36292,36366,27053,36280,35935,35928,23070,36444,35767,36142,27977,35693,36307,36263,36144,35557,35851,36208,35982,26653,36215,35903,35827,36383,22814,36488,36436,36232,36257,36576,23192,36313,35964,36093,28177,36201,36312,36399,36437,36019,36701,23261,36236,35304,35550,35573,36041,36516,35619,21390,36130,36035,36079,36250,35642,36014,36181,36409,36750,35194,36231,36621,36347,36708,36116,22442,35953,36238,24521,35903,36478,36302,26867,36033,36691,36598,36169,29117,36562,36571,36674,36378,26458,36543,36431,36399,30229,36514,36013,36541,33897,36630,36824,36736,36572,20268,36893,36358,36432,36723,36302,28115,35842,35970,35902,19610,34814,35632,35533,36022,36000,35912,35708,35671,23616,35779,36080,35910,35566,25713,37388,35921,36138,36457,31997,36030,36115,36086,36260,35458,36385,35812,36034,23302,35894,35995,36040,35737,19474,36157,36232,36197,36086,25537,36164,36521,36722,36354,27824,36216,35943,36057,36431,24596,36344,36383,36174,37202,36268,36343,36330,25630,36276,36036,36243,35932,32898,36324,36421,35353,33981,36014,36132,36070,36261,36038,35888,35384,35378,31220,35060,35657,36317,35876,19901,36044,36266,35401,35790,22612,35901,36038,35833,35803,31059,36014,36025,35942,30394,35751,36363,36049,35552,36079,35527,35410,25680,35971,35707,27151,36267,35802,3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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/genomes/gnomad.genomes.mt/cols\",\"_spec\":{\"name\":\"TableSpec\",\"file_version\":65536,\"hail_version\":\"devel-b12fb4564562\",\"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\":[20314]}}}}")))))) (Let __iruid_907 (ArrayMap __iruid_908 (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (Let __iruid_909 (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_908)) (If (Coalesce (GetField adj (Ref __iruid_909)) (False)) (Ref __iruid_909) (NA Struct{GT:Call,adj:Boolean})))) (InsertFields (Ref row) ("locus" "alleles" "the entries! [877f12a8827e18f61222c6c8c5fb04a8]") (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap __iruid_910 (ArrayRange (I32 0) (ArrayLen (GetField __cols (Ref global))) (I32 1)) (SelectFields (GT) (ArrayRef (Ref __iruid_907) (Ref __iruid_910)))))))) (Let __iruid_911 (ToDict (ArrayMap __iruid_912 (GetField rows (TableCollect (TableKeyBy () False (TableRead Table{global:Struct{},key:[s],row:Struct{s:String,release:Boolean}} False "{\"name\":\"TableNativeReader\",\"path\":\"gs://gnomad/metadata/genomes/gnomad.genomes.metadata.2018-10-11.ht\",\"_spec\":null}")))) (MakeTuple (0 1) (SelectFields (s) (Ref __iruid_912)) (SelectFields (release) (Ref __iruid_912))))) (Let __iruid_913 (ArrayMap __iruid_914 (GetField __cols (Ref global)) (InsertFields (Ref __iruid_914) None (__uid_12 (ApplyIR get Struct{release:Boolean} (Ref __iruid_911) (MakeStruct (s (GetField s (Ref __iruid_914)))))))) (Let __iruid_915 (ArrayMap __iruid_916 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_913)) (I32 1)) (Let __iruid_917 (ArrayRef (Ref __iruid_913) (Ref __iruid_916)) (InsertFields (SelectFields () (Ref __iruid_917)) None (meta (GetField __uid_12 (Ref __iruid_917)))))) (InsertFields (Ref global) ("__cols" "newColIdx") (newColIdx (ArrayFilter __iruid_918 (ArrayRange (I32 0) (ArrayLen (Ref __iruid_915)) (I32 1)) (Coalesce (GetField release (GetField meta (ArrayRef (Ref __iruid_915) (Ref __iruid_918)))) (False))))))))) (InsertFields (Ref row) None (`the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (ArrayMap __iruid_919 (GetField newColIdx (Ref global)) (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_919)))))) (SelectFields () (Ref global)))) (ArrayAgg __iruid_920 (ArrayFilter __iruid_921 (ArrayRange (I32 0) (ArrayLen (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row))) (I32 1)) (ApplyUnaryPrimOp Bang (IsNA (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_921))))) (MakeStruct (__uid_16 (ApplyComparisonOp GT (ApplyAggOp Sum () None ( (Apply toInt64 Int64 (Apply isNonRef Boolean (GetField GT (ArrayRef (GetField `the entries! [877f12a8827e18f61222c6c8c5fb04a8]` (Ref row)) (Ref __iruid_920))))))) (I64 0)))))) (Coalesce (GetField __uid_16 (Ref row)) (False)))) 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_37. instruction count: 3 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_37.apply instruction count: 7 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_37.apply instruction count: 12 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_37.DECODE_r_struct_of_END_TO_r_tuple_of_END_1 instruction count: 14 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38. instruction count: 3 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.apply instruction count: 7 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.apply instruction count: 12 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.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_int32ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryENDANDo_int32ANDo_boolEND_TO_o_tuple_of_o_locusANDo_array_of_o_stringEND_1 instruction count: 155 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.INPLACE_DECODE_o_struct_of_r_binaryANDr_int32END_TO_o_tuple_of_r_binaryANDr_int32END_2 instruction count: 22 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.INPLACE_DECODE_r_binary_TO_r_binary_3 instruction count: 29 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.INPLACE_DECODE_r_int32_TO_r_int32_4 instruction count: 8 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.INPLACE_DECODE_o_array_of_o_binary_TO_o_array_of_o_binary_5 instruction count: 99 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.INPLACE_DECODE_o_binary_TO_o_binary_6 instruction count: 29 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_binary_7 instruction count: 9 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_float64_8 instruction count: 5 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_array_of_o_binary_9 instruction count: 54 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.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_int32ANDo_float64ANDo_boolANDo_boolANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_float64ANDo_binaryEND_10 instruction count: 386 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_array_of_o_int32_11 instruction count: 54 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_int32_12 instruction count: 5 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_array_of_o_float64_13 instruction count: 54 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_38.SKIP_o_bool_14 instruction count: 5 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39. instruction count: 3 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.apply instruction count: 7 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.apply instruction count: 12 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.DECODE_o_struct_of_o_array_of_o_struct_of_o_int32ANDo_binaryANDo_boolENDEND_TO_o_tuple_of_o_array_of_o_tuple_of_o_callANDo_boolENDEND_1 instruction count: 46 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_array_of_o_struct_of_o_int32ANDo_binaryANDo_boolEND_TO_o_array_of_o_tuple_of_o_int32ANDo_boolEND_2 instruction count: 99 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_struct_of_o_int32ANDo_binaryANDo_boolEND_TO_o_tuple_of_o_int32ANDo_boolEND_3 instruction count: 79 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_int32_TO_o_int32_4 instruction count: 8 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.SKIP_o_binary_5 instruction count: 9 2019-10-08 20:52:20 root: INFO: is/hail/codegen/generated/C_etypeDecode_39.INPLACE_DECODE_o_bool_TO_o_bool_6 instruction count: 8 2019-10-08 20:52:20 root: ERROR: RuntimeException: globals mismatch: typ: Struct{} val: +Struct{} From java.lang.RuntimeException: globals mismatch: typ: Struct{} val: +Struct{} at is.hail.expr.ir.TableValue.(TableValue.scala:50) 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.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableMapGlobals.execute(TableIR.scala:1120) at is.hail.expr.ir.TableKeyBy.execute(TableIR.scala:366) at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:964) at is.hail.expr.ir.TableFilter.execute(TableIR.scala:439) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply$mcJ$sp(Interpret.scala:744) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:744) at is.hail.expr.ir.Interpret$$anonfun$apply$2.apply(Interpret.scala:744) at scala.Option.getOrElse(Option.scala:121) at is.hail.expr.ir.Interpret$.apply(Interpret.scala:744) 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$$anonfun$execute$1.apply(Backend.scala:57) at is.hail.backend.Backend$$anonfun$execute$1.apply(Backend.scala:57) 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:57) at is.hail.backend.Backend.executeJSON(Backend.scala:63) 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) 2019-10-08 20:53:18 ExecutorAllocationManager: INFO: Request to remove executorIds: 1