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olavurmortensen/hail_error

Created July 2, 2021 13:12
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hail_error
---------------------------------------------------------------------------
FatalError Traceback (most recent call last)
<ipython-input-80-accb05dc05de> in <module>
----> 1 hl.len(mt.AD).summarize()
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/expr/expressions/base_expression.py in summarize(self, handler)
1102 if handler is None:
1103 handler = hl.utils.default_handler()
-> 1104 handler(self._summarize(name=prefix))
1105
1106 def _selector_and_agg_method(self):
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/expr/expressions/base_expression.py in _summarize(self, agg_res, name, header, top)
1075 raise ValueError("Cannot summarize a scalar expression")
1076 if agg_res is None:
-> 1077 count, agg_res = self._aggregation_method()(hl.tuple((hl.agg.count(), self._all_summary_aggs())))
1078 summary_header = f'{count} records.'
1079 sum_fields, nested = self._summary_fields(agg_res, top)
<decorator-gen-1216> in aggregate_entries(self, expr, _localize)
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
612 def wrapper(__original_func, *args, **kwargs):
613 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 614 return __original_func(*args_, **kwargs_)
615
616 return wrapper
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/matrixtable.py in aggregate_entries(self, expr, _localize)
2079 agg_ir = ir.MatrixAggregate(base._mir, expr._ir)
2080 if _localize:
-> 2081 return Env.backend().execute(agg_ir)
2082 else:
2083 return construct_expr(ir.LiftMeOut(agg_ir), expr.dtype)
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed)
96 raise HailUserError(message_and_trace) from None
97
---> 98 raise e
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed)
72 # print(self._hail_package.expr.ir.Pretty.apply(jir, True, -1))
73 try:
---> 74 result = json.loads(self._jhc.backend().executeJSON(jir))
75 value = ir.typ._from_json(result['value'])
76 timings = result['timings']
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/py4j/java_gateway.py in __call__(self, *args)
1255 answer = self.gateway_client.send_command(command)
1256 return_value = get_return_value(
-> 1257 answer, self.gateway_client, self.target_id, self.name)
1258
1259 for temp_arg in temp_args:
/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs)
30 raise FatalError('%s\n\nJava stack trace:\n%s\n'
31 'Hail version: %s\n'
---> 32 'Error summary: %s' % (deepest, full, hail.__version__, deepest), error_id) from None
33 except pyspark.sql.utils.CapturedException as e:
34 raise FatalError('%s\n\nJava stack trace:\n%s\n'
FatalError: HailException: array index out of bounds: index=1, length=1
----------
Python traceback:
File "<ipython-input-75-49c8349cc875>", line 1, in <module>
mt = hl.split_multi_hts(mt)
File "<decorator-gen-1708>", line 2, in split_multi_hts
File "/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/methods/statgen.py", line 1827, in split_multi_hts
[hl.sum(split.AD) - split.AD[split.a_index], split.AD[split.a_index]])
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 7 in stage 23.0 failed 1 times, most recent failure: Lost task 7.0 in stage 23.0 (TID 722, localhost, executor driver): is.hail.utils.HailException: array index out of bounds: index=1, length=1
----------
Python traceback:
File "<ipython-input-75-49c8349cc875>", line 1, in <module>
mt = hl.split_multi_hts(mt)
File "<decorator-gen-1708>", line 2, in split_multi_hts
File "/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/methods/statgen.py", line 1827, in split_multi_hts
[hl.sum(split.AD) - split.AD[split.a_index], split.AD[split.a_index]])
at __C5100CompiledWithAggs.applyregion17_58(Emit.scala:765)
at __C5100CompiledWithAggs.apply(Emit.scala)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply$mcVJ$sp(Interpret.scala:921)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply(Interpret.scala:920)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply(Interpret.scala:920)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at is.hail.expr.ir.Interpret$.is$hail$expr$ir$Interpret$$itF$1(Interpret.scala:920)
at is.hail.expr.ir.Interpret$$anonfun$29.apply(Interpret.scala:939)
at is.hail.expr.ir.Interpret$$anonfun$29.apply(Interpret.scala:939)
at is.hail.rvd.RVD$$anonfun$20.apply(RVD.scala:691)
at is.hail.rvd.RVD$$anonfun$20.apply(RVD.scala:691)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:59)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:59)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:68)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:445)
at is.hail.utils.package$.singletonElement(package.scala:644)
at is.hail.rvd.RVD$$anonfun$combine$1.apply(RVD.scala:724)
at is.hail.rvd.RVD$$anonfun$combine$1.apply(RVD.scala:724)
at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2158)
at is.hail.rvd.RVD.combine(RVD.scala:724)
at is.hail.expr.ir.Interpret$.run(Interpret.scala:938)
at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:354)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:338)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:335)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:25)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:23)
at is.hail.utils.package$.using(package.scala:618)
at is.hail.annotations.Region$.scoped(Region.scala:18)
at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:23)
at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:247)
at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:335)
at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:379)
at is.hail.backend.spark.SparkBackend$$anonfun$7.apply(SparkBackend.scala:377)
at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)
at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:377)
at sun.reflect.GeneratedMethodAccessor182.invoke(Unknown Source)
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)
is.hail.utils.HailException: array index out of bounds: index=1, length=1
----------
Python traceback:
File "<ipython-input-75-49c8349cc875>", line 1, in <module>
mt = hl.split_multi_hts(mt)
File "<decorator-gen-1708>", line 2, in split_multi_hts
File "/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/methods/statgen.py", line 1827, in split_multi_hts
[hl.sum(split.AD) - split.AD[split.a_index], split.AD[split.a_index]])
at __C5100CompiledWithAggs.applyregion17_58(Emit.scala:765)
at __C5100CompiledWithAggs.apply(Emit.scala)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply$mcVJ$sp(Interpret.scala:921)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply(Interpret.scala:920)
at is.hail.expr.ir.Interpret$$anonfun$is$hail$expr$ir$Interpret$$itF$1$1.apply(Interpret.scala:920)
at scala.collection.Iterator$class.foreach(Iterator.scala:891)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
at is.hail.expr.ir.Interpret$.is$hail$expr$ir$Interpret$$itF$1(Interpret.scala:920)
at is.hail.expr.ir.Interpret$$anonfun$29.apply(Interpret.scala:939)
at is.hail.expr.ir.Interpret$$anonfun$29.apply(Interpret.scala:939)
at is.hail.rvd.RVD$$anonfun$20.apply(RVD.scala:691)
at is.hail.rvd.RVD$$anonfun$20.apply(RVD.scala:691)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:59)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$2.apply(RichContextRDD.scala:59)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:68)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:445)
at is.hail.utils.package$.singletonElement(package.scala:644)
at is.hail.rvd.RVD$$anonfun$combine$1.apply(RVD.scala:724)
at is.hail.rvd.RVD$$anonfun$combine$1.apply(RVD.scala:724)
at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
at org.apache.spark.SparkContext$$anonfun$36.apply(SparkContext.scala:2157)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Hail version: 0.2.61-3c86d3ba497a
Error summary: HailException: array index out of bounds: index=1, length=1
----------
Python traceback:
File "<ipython-input-75-49c8349cc875>", line 1, in <module>
mt = hl.split_multi_hts(mt)
File "<decorator-gen-1708>", line 2, in split_multi_hts
File "/opt/conda/envs/fargen-1-exome/lib/python3.7/site-packages/hail/methods/statgen.py", line 1827, in split_multi_hts
[hl.sum(split.AD) - split.AD[split.a_index], split.AD[split.a_index]])
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