Hi there, I’m trying to export a vcf but the SparkContext is shutting down. What should I do bout it?
Here is the trace back:
hl.export_vcf(dataset_result, 'chr22.vcf.bgz')
2018-06-14 16:42:24 Hail: WARN: export_vcf found no row field 'info'. Emitting no INFO fields.
[Stage 1:> (0 + 28) / 350]---------------------------------------------------------------------------
FatalError Traceback (most recent call last)
<ipython-input-5-64146574f444> in <module>()
----> 1 hl.export_vcf(dataset_result, 'chr22.vcf.bgz')
~/bin/hail/python/hail/typecheck/check.py in wrapper(*args, **kwargs)
545 def wrapper(*args, **kwargs):
546 args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547 return f(*args_, **kwargs_)
548
549 update_wrapper(wrapper, f)
~/bin/hail/python/hail/methods/impex.py in export_vcf(dataset, output, append_to_header, parallel, metadata)
420 Env.hail().io.vcf.ExportVCF.apply(dataset._jvds, output, joption(append_to_header),
421 Env.hail().utils.ExportType.getExportType(parallel),
--> 422 joption(typ._convert_to_j(metadata)))
423
424
~/bin/spark-2.2.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__(self, *args)
1131 answer = self.gateway_client.send_command(command)
1132 return_value = get_return_value(
-> 1133 answer, self.gateway_client, self.target_id, self.name)
1134
1135 for temp_arg in temp_args:
~/bin/hail/python/hail/utils/java.py in deco(*args, **kwargs)
194 raise FatalError('%s\n\nJava stack trace:\n%s\n'
195 'Hail version: %s\n'
--> 196 'Error summary: %s' % (deepest, full, hail.__version__, deepest)) from None
197 except pyspark.sql.utils.CapturedException as e:
198 raise FatalError('%s\n\nJava stack trace:\n%s\n'
FatalError: SparkException: Job 1 cancelled because SparkContext was shut down
Java stack trace:
org.apache.spark.SparkException: Job 1 cancelled because SparkContext was shut down
at org.apache.spark.scheduler.DAGScheduler$$anonfun$cleanUpAfterSchedulerStop$1.apply(DAGScheduler.scala:820)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$cleanUpAfterSchedulerStop$1.apply(DAGScheduler.scala:818)
at scala.collection.mutable.HashSet.foreach(HashSet.scala:78)
at org.apache.spark.scheduler.DAGScheduler.cleanUpAfterSchedulerStop(DAGScheduler.scala:818)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onStop(DAGScheduler.scala:1732)
at org.apache.spark.util.EventLoop.stop(EventLoop.scala:83)
at org.apache.spark.scheduler.DAGScheduler.stop(DAGScheduler.scala:1651)
at org.apache.spark.SparkContext$$anonfun$stop$8.apply$mcV$sp(SparkContext.scala:1921)
at org.apache.spark.util.Utils$.tryLogNonFatalError(Utils.scala:1317)
at org.apache.spark.SparkContext.stop(SparkContext.scala:1920)
at org.apache.spark.SparkContext$$anonfun$2.apply$mcV$sp(SparkContext.scala:581)
at org.apache.spark.util.SparkShutdownHook.run(ShutdownHookManager.scala:216)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ShutdownHookManager.scala:188)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1$$anonfun$apply$mcV$sp$1.apply(ShutdownHookManager.scala:188)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1$$anonfun$apply$mcV$sp$1.apply(ShutdownHookManager.scala:188)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1954)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1.apply$mcV$sp(ShutdownHookManager.scala:188)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1.apply(ShutdownHookManager.scala:188)
at org.apache.spark.util.SparkShutdownHookManager$$anonfun$runAll$1.apply(ShutdownHookManager.scala:188)
at scala.util.Try$.apply(Try.scala:192)
at org.apache.spark.util.SparkShutdownHookManager.runAll(ShutdownHookManager.scala:188)
at org.apache.spark.util.SparkShutdownHookManager$$anon$2.run(ShutdownHookManager.scala:178)
at org.apache.hadoop.util.ShutdownHookManager$1.run(ShutdownHookManager.java:54)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2075)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1151)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1.apply(PairRDDFunctions.scala:1096)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1.apply(PairRDDFunctions.scala:1096)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.PairRDDFunctions.saveAsHadoopDataset(PairRDDFunctions.scala:1096)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$4.apply$mcV$sp(PairRDDFunctions.scala:1070)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$4.apply(PairRDDFunctions.scala:1035)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$4.apply(PairRDDFunctions.scala:1035)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.PairRDDFunctions.saveAsHadoopFile(PairRDDFunctions.scala:1035)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$3.apply$mcV$sp(PairRDDFunctions.scala:1016)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$3.apply(PairRDDFunctions.scala:1016)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$3.apply(PairRDDFunctions.scala:1016)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.PairRDDFunctions.saveAsHadoopFile(PairRDDFunctions.scala:1015)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:973)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$2.apply(PairRDDFunctions.scala:971)
at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopFile$2.apply(PairRDDFunctions.scala:971)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.PairRDDFunctions.saveAsHadoopFile(PairRDDFunctions.scala:971)
at org.apache.spark.rdd.RDD$$anonfun$saveAsTextFile$2.apply$mcV$sp(RDD.scala:1507)
at org.apache.spark.rdd.RDD$$anonfun$saveAsTextFile$2.apply(RDD.scala:1495)
at org.apache.spark.rdd.RDD$$anonfun$saveAsTextFile$2.apply(RDD.scala:1495)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.saveAsTextFile(RDD.scala:1495)
at is.hail.utils.richUtils.RichRDD$.writeTable$extension(RichRDD.scala:66)
at is.hail.io.vcf.ExportVCF$.apply(ExportVCF.scala:426)
at is.hail.io.vcf.ExportVCF.apply(ExportVCF.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:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:748)
Hail version: devel-d53ebc1b9cbf
Error summary: SparkException: Job 1 cancelled because SparkContext was shut down