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October 1, 2016 14:22
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| hail: info: running: read -i file:///mnt/lustre/mzekavat/MESA_VIRGO/rawVDS/raw_MESA_VIRGO.vds | |
| [Stage 1:======================================================>(159 + 1) / 160]hail: info: running: filtervariants expr -c 'v.contig == "X"' --keep | |
| hail: info: running: filtersamples expr -c '"^NW" ~ s.id' --keep | |
| hail: info: running: filtersamples list --remove -i file:///mnt/lustre/mzekavat/MESA_VIRGO/MESA_ONLY/QCed_VDS/MESA_badSamples_Cvg30_Contam3.txt | |
| hail: info: running: filtervariants intervals -i file:///mnt/lustre/aganna/LCR.interval_list --remove | |
| hail: info: running: filtervariants expr -c va.pass --keep | |
| hail: info: running: filtergenotypes -c '(g.ad[0] + g.ad[1]) / g.dp < 0.9 || (g.isHomRef && (g.ad[0] / g.dp < 0.9 || g.gq < 20)) || (g.isHet && (g.ad[1] / g.dp < 0.20 || g.pl[0] < 20)) || (g.isHomVar && (g.ad[1] / g.dp < 0.9 || g.pl[0] < 20)) || g.dp > 200' --remove | |
| hail: info: running: variantqc | |
| hail: info: running: filtervariants expr -c '((va.info.QD > 3 && v.altAllele.isIndel) || (va.info.QD > 2 && v.altAllele.isSNP)) && (va.qc.callRate > 0.95) && va.qc.dpMean > 20 && va.qc.AF > 0.1' --keep | |
| hail: info: running: imputesex -m 0.05 | |
| [Stage 3:> (0 + 160) / 197961]hail: imputesex: caught exception: org.apache.spark.SparkException: Job aborted due to stage failure: Task 89 in stage 3.0 failed 4 times, most recent failure: Lost task 89.3 in stage 3.0 (TID 198306, nid00003.urika.com): org.apache.spark.SparkException: Error communicating with MapOutputTracker | |
| at org.apache.spark.MapOutputTracker.askTracker(MapOutputTracker.scala:113) | |
| at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:167) | |
| at org.apache.spark.shuffle.hash.HashShuffleReader.read(HashShuffleReader.scala:47) | |
| at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:90) | |
| at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:300) | |
| at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) | |
| at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) | |
| at org.apache.spark.scheduler.Task.run(Task.scala:88) | |
| at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) | |
| at java.lang.Thread.run(Thread.java:745) | |
| Caused by: org.apache.spark.SparkException: Error sending message [message = GetMapOutputStatuses(0)] | |
| at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:118) | |
| at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:77) | |
| at org.apache.spark.MapOutputTracker.askTracker(MapOutputTracker.scala:109) | |
| ... 11 more | |
| Caused by: org.apache.spark.SparkException: Map output statuses were 192902832 bytes which exceeds spark.akka.frameSize (134217728 bytes). | |
| at org.apache.spark.MapOutputTrackerMasterEndpoint$$anonfun$receiveAndReply$1.applyOrElse(MapOutputTracker.scala:57) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$processMessage(AkkaRpcEnv.scala:177) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1$$anonfun$applyOrElse$4.apply$mcV$sp(AkkaRpcEnv.scala:126) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$safelyCall(AkkaRpcEnv.scala:197) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1.applyOrElse(AkkaRpcEnv.scala:125) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:59) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:42) | |
| at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:118) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.applyOrElse(ActorLogReceive.scala:42) | |
| at akka.actor.Actor$class.aroundReceive(Actor.scala:467) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1.aroundReceive(AkkaRpcEnv.scala:92) | |
| at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516) | |
| at akka.actor.ActorCell.invoke(ActorCell.scala:487) | |
| at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238) | |
| at akka.dispatch.Mailbox.run(Mailbox.scala:220) | |
| at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397) | |
| at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) | |
| at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) | |
| at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) | |
| at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) | |
| Driver stacktrace: | |
| at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1283) | |
| at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1271) | |
| at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1270) | |
| at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) | |
| at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47) | |
| at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1270) | |
| at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:697) | |
| at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:697) | |
| at scala.Option.foreach(Option.scala:236) | |
| at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:697) | |
| at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1496) | |
| at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1458) | |
| at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1447) | |
| at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) | |
| at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:567) | |
| at org.apache.spark.SparkContext.runJob(SparkContext.scala:1824) | |
| at org.apache.spark.SparkContext.runJob(SparkContext.scala:1837) | |
| at org.apache.spark.SparkContext.runJob(SparkContext.scala:1850) | |
| at org.apache.spark.SparkContext.runJob(SparkContext.scala:1921) | |
| at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:909) | |
| at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147) | |
| at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108) | |
| at org.apache.spark.rdd.RDD.withScope(RDD.scala:310) | |
| at org.apache.spark.rdd.RDD.collect(RDD.scala:908) | |
| at org.broadinstitute.hail.methods.ImputeSexPlink$.apply(ImputeSexPlink.scala:72) | |
| at org.broadinstitute.hail.driver.ImputeSex$.run(ImputeSex.scala:43) | |
| at org.broadinstitute.hail.driver.ImputeSex$.run(ImputeSex.scala:6) | |
| at org.broadinstitute.hail.driver.Command.runCommand(Command.scala:245) | |
| at org.broadinstitute.hail.driver.Main$.runCommand(Main.scala:122) | |
| at org.broadinstitute.hail.driver.Main$$anonfun$runCommands$1$$anonfun$1.apply(Main.scala:146) | |
| at org.broadinstitute.hail.driver.Main$$anonfun$runCommands$1$$anonfun$1.apply(Main.scala:146) | |
| at org.broadinstitute.hail.utils.package$.time(package.scala:55) | |
| at org.broadinstitute.hail.driver.Main$$anonfun$runCommands$1.apply(Main.scala:145) | |
| at org.broadinstitute.hail.driver.Main$$anonfun$runCommands$1.apply(Main.scala:139) | |
| at scala.collection.IndexedSeqOptimized$class.foldl(IndexedSeqOptimized.scala:51) | |
| at scala.collection.IndexedSeqOptimized$class.foldLeft(IndexedSeqOptimized.scala:60) | |
| at scala.collection.mutable.ArrayOps$ofRef.foldLeft(ArrayOps.scala:108) | |
| at org.broadinstitute.hail.driver.Main$.runCommands(Main.scala:139) | |
| at org.broadinstitute.hail.driver.Main$.main(Main.scala:307) | |
| at org.broadinstitute.hail.driver.Main.main(Main.scala) | |
| 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:497) | |
| at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674) | |
| at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180) | |
| at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205) | |
| at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120) | |
| at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)org.apache.spark.SparkException: Error communicating with MapOutputTracker | |
| at org.apache.spark.MapOutputTracker.askTracker(MapOutputTracker.scala:113) | |
| at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:167) | |
| at org.apache.spark.shuffle.hash.HashShuffleReader.read(HashShuffleReader.scala:47) | |
| at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:90) | |
| at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:300) | |
| at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) | |
| at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) | |
| at org.apache.spark.scheduler.Task.run(Task.scala:88) | |
| at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) | |
| at java.lang.Thread.run(Thread.java:745)org.apache.spark.SparkException: Error sending message [message = GetMapOutputStatuses(0)] | |
| at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:118) | |
| at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:77) | |
| at org.apache.spark.MapOutputTracker.askTracker(MapOutputTracker.scala:109) | |
| at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:167) | |
| at org.apache.spark.shuffle.hash.HashShuffleReader.read(HashShuffleReader.scala:47) | |
| at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:90) | |
| at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:300) | |
| at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) | |
| at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) | |
| at org.apache.spark.scheduler.Task.run(Task.scala:88) | |
| at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) | |
| at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) | |
| at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) | |
| at java.lang.Thread.run(Thread.java:745)org.apache.spark.SparkException: Map output statuses were 192902832 bytes which exceeds spark.akka.frameSize (134217728 bytes). | |
| at org.apache.spark.MapOutputTrackerMasterEndpoint$$anonfun$receiveAndReply$1.applyOrElse(MapOutputTracker.scala:57) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$processMessage(AkkaRpcEnv.scala:177) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1$$anonfun$applyOrElse$4.apply$mcV$sp(AkkaRpcEnv.scala:126) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$safelyCall(AkkaRpcEnv.scala:197) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1.applyOrElse(AkkaRpcEnv.scala:125) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33) | |
| at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:59) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:42) | |
| at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:118) | |
| at org.apache.spark.util.ActorLogReceive$$anon$1.applyOrElse(ActorLogReceive.scala:42) | |
| at akka.actor.Actor$class.aroundReceive(Actor.scala:467) | |
| at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1.aroundReceive(AkkaRpcEnv.scala:92) | |
| at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516) | |
| at akka.actor.ActorCell.invoke(ActorCell.scala:487) | |
| at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238) | |
| at akka.dispatch.Mailbox.run(Mailbox.scala:220) | |
| at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397) | |
| at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) | |
| at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) | |
| at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) | |
| at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) |
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