NullPointerException

Hail Query & hailctl
1

I am having a consistent issue with running into NullPointerExceptions that I don’t know how to debug.

The issue arises after the following annotation and filtering step:

  ht = ht.explode(ht.microexon_interval_identifier)

  event_split = ht.microexon_interval_identifier.first_match_in(r"(HsaEX\d{7}|putative_microexon_\d{9})(?:_(.*))?")

  ht = ht.annotate(event=event_split[0], event_region=event_split[1])

  ht = ht.annotate(
    is_flanking_exon=((ht.microexon_interval_identifier.contains('c1')) |
                      (ht.microexon_interval_identifier.contains('c2'))) &
                     (ht.microexon_interval_identifier.startswith('HsaEX')),
    is_microexon=(~ht.microexon_interval_identifier.contains('c1')) &
                 (~ht.microexon_interval_identifier.contains('c2')) &
                 (ht.microexon_interval_identifier.startswith('HsaEX')),
    is_novel_microexon=novel_microexons_set.contains(ht.event)
  )

  ht = ht.filter(ht.is_flanking_exon | ht.is_microexon | ht.is_novel_microexon)

The traceback is

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_umd.py", line 198, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/Users/hannes/hail/process_all_dataset_jointly.py", line 129, in <module>
    ht = ht.checkpoint("/Users/hannes/Desktop/mssng_cg_checkpoint.ht", overwrite=True)
  File "<decorator-gen-1010>", line 2, in checkpoint
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 577, in wrapper
    return __original_func(*args_, **kwargs_)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/table.py", line 1238, in checkpoint
    self.write(output=output, overwrite=overwrite, stage_locally=stage_locally, _codec_spec=_codec_spec)
  File "<decorator-gen-1012>", line 2, in write
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 577, in wrapper
    return __original_func(*args_, **kwargs_)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/table.py", line 1271, in write
    Env.backend().execute(ir.TableWrite(self._tir, ir.TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 110, in execute
    raise e
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 86, in execute
    result_tuple = self._jhc.backend().executeEncode(jir, stream_codec)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/py4j/java_gateway.py", line 1305, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 31, in deco
    'Error summary: %s' % (deepest, full, hail.__version__, deepest), error_id) from None
hail.utils.java.FatalError: NullPointerException: null
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 6 in stage 4.0 failed 1 times, most recent failure: Lost task 6.0 in stage 4.0 (TID 536) (192.168.4.98 executor driver): java.lang.NullPointerException
	at __C1178collect_distributed_array.__m1336ENCODE_SJavaString$_TO_o_binary(Unknown Source)
	at __C1178collect_distributed_array.__m1324ENCODE_SInsertFieldsStruct_TO_r_struct_of_o_binaryANDo_int32ANDo_binaryANDo_int32ANDo_int32ANDo_int32ANDo_binaryANDo_float64ANDo_int32ANDo_binaryANDo_boolANDo_binaryANDr_binaryANDr_binaryANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDo_binaryANDo_binaryANDr_boolANDr_boolANDo_boolEND(Unknown Source)
	at __C1178collect_distributed_array.__m1190split_WritePartition(Unknown Source)
	at __C1178collect_distributed_array.apply(Unknown Source)
	at __C1178collect_distributed_array.apply(Unknown Source)
	at is.hail.backend.BackendUtils.$anonfun$collectDArray$2(BackendUtils.scala:31)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.annotations.RegionPool.scopedRegion(RegionPool.scala:144)
	at is.hail.backend.BackendUtils.$anonfun$collectDArray$1(BackendUtils.scala:30)
	at is.hail.backend.spark.SparkBackendComputeRDD.compute(SparkBackend.scala:730)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:131)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2258)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2207)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2206)
	at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
	at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2206)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1079)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1079)
	at scala.Option.foreach(Option.scala:407)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1079)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2445)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2387)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2376)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:868)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2196)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2217)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2236)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2261)
	at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:1030)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:414)
	at org.apache.spark.rdd.RDD.collect(RDD.scala:1029)
	at is.hail.backend.spark.SparkBackend.parallelizeAndComputeWithIndex(SparkBackend.scala:286)
	at is.hail.backend.BackendUtils.collectDArray(BackendUtils.scala:28)
	at __C1151Compiled.apply(Emit.scala)
	at is.hail.expr.ir.CompileAndEvaluate$.$anonfun$_apply$3(CompileAndEvaluate.scala:57)
	at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
	at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:57)
	at is.hail.expr.ir.CompileAndEvaluate$.evalToIR(CompileAndEvaluate.scala:30)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:30)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:67)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72)
	at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69)
	at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$3(LoweringPass.scala:16)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
	at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$1(LoweringPass.scala:16)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
	at is.hail.expr.ir.lowering.LoweringPass.apply(LoweringPass.scala:14)
	at is.hail.expr.ir.lowering.LoweringPass.apply$(LoweringPass.scala:13)
	at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64)
	at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:15)
	at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:13)
	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
	at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:38)
	at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13)
	at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:47)
	at is.hail.backend.spark.SparkBackend._execute(SparkBackend.scala:381)
	at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:417)
	at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17)
	at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:46)
	at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275)
	at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:414)
	at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)
	at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:413)
	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 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:745)
java.lang.NullPointerException: null
	at __C1178collect_distributed_array.__m1336ENCODE_SJavaString$_TO_o_binary(Unknown Source)
	at __C1178collect_distributed_array.__m1324ENCODE_SInsertFieldsStruct_TO_r_struct_of_o_binaryANDo_int32ANDo_binaryANDo_int32ANDo_int32ANDo_int32ANDo_binaryANDo_float64ANDo_int32ANDo_binaryANDo_boolANDo_binaryANDr_binaryANDr_binaryANDr_struct_of_r_struct_of_r_binaryANDr_int32ENDANDr_array_of_r_binaryENDANDo_binaryANDo_binaryANDr_boolANDr_boolANDo_boolEND(Unknown Source)
	at __C1178collect_distributed_array.__m1190split_WritePartition(Unknown Source)
	at __C1178collect_distributed_array.apply(Unknown Source)
	at __C1178collect_distributed_array.apply(Unknown Source)
	at is.hail.backend.BackendUtils.$anonfun$collectDArray$2(BackendUtils.scala:31)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.annotations.RegionPool.scopedRegion(RegionPool.scala:144)
	at is.hail.backend.BackendUtils.$anonfun$collectDArray$1(BackendUtils.scala:30)
	at is.hail.backend.spark.SparkBackendComputeRDD.compute(SparkBackend.scala:730)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:131)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Hail version: 0.2.78-b17627756568
Error summary: NullPointerException: null

I’d be very thankful for any help on how to debug this.

2

This is a Hail bug, not a you bug.

I suspect you can avoid this for now by doing the following at the top of your script:

hl._set_flags(no_whole_stage_codegen='1')

However, I’d like to fix this issue since the new execution strategy that has the bug also has some major improvements over the old execution strategy.

Is there any chance the pipeline uses public data / can be shared?

3

Thanks for the tip. Setting the flag seems to have fixed this part of the pipeline, but now I get a NullPointerException again in the very next step of the pipeline which is

  mt = ht.to_matrix_table(row_key=['variant', 'microexon_interval_identifier', "event", "event_region"],
                          row_fields=['distance_spliceJunction', 'gene_symbol', 'alt_fraction',
                                      'damaging_missense_count', 'spliceAI_category', 'is_flanking_exon',
                                      'is_microexon', 'is_novel_microexon'],
                          col_key=["sample_id"],
                          col_fields=["dataset"])

Since you said that you changed the execution strategy, could I try a workaround by downgrading hail?

I’m afraid our data isn’t public, but I can the full script with you if that helps.

4

Can you share the stack trace for the new error?

5 
mt.count()
Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/matrixtable.py", line 2441, in count
    return Env.backend().execute(count_ir)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 110, in execute
    raise e
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 86, in execute
    result_tuple = self._jhc.backend().executeEncode(jir, stream_codec)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/py4j/java_gateway.py", line 1305, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/Users/hannes/opt/anaconda3/envs/hail/lib/python3.7/site-packages/hail/backend/py4j_backend.py", line 31, in deco
    'Error summary: %s' % (deepest, full, hail.__version__, deepest), error_id) from None
hail.utils.java.FatalError: NullPointerException: null
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 8 in stage 15.0 failed 1 times, most recent failure: Lost task 8.0 in stage 15.0 (TID 3169) (192.168.4.98 executor driver): java.lang.NullPointerException
	at __C4220Compiled.apply(Emit.scala)
	at is.hail.expr.ir.TableMapRows.$anonfun$execute$43(TableIR.scala:2031)
	at scala.runtime.java8.JFunction1$mcJJ$sp.apply(JFunction1$mcJJ$sp.java:23)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:512)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at is.hail.io.RichContextRDDLong$$anon$3.hasNext(RichContextRDDRegionValue.scala:196)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:1087)
	at is.hail.utils.richUtils.RichIterator$$anon$1.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.BufferedAggregatorIterator.next(BufferedAggregatorIterator.scala:41)
	at is.hail.utils.BufferedAggregatorIterator.next(BufferedAggregatorIterator.scala:9)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:494)
	at is.hail.utils.richUtils.RichContextRDD$$anon$1.next(RichContextRDD.scala:77)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:494)
	at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:194)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
	at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52)
	at org.apache.spark.scheduler.Task.run(Task.scala:131)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2258)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2207)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2206)
	at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
	at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2206)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1079)
	at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1079)
	at scala.Option.foreach(Option.scala:407)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1079)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2445)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2387)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2376)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:868)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2196)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2217)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2249)
	at is.hail.sparkextras.ContextRDD.crunJobWithIndex(ContextRDD.scala:238)
	at is.hail.rvd.RVD$.getKeyInfo(RVD.scala:1231)
	at is.hail.rvd.RVD$.makeCoercer(RVD.scala:1306)
	at is.hail.rvd.RVD$.coerce(RVD.scala:1262)
	at is.hail.rvd.RVD$.coerce(RVD.scala:1246)
	at is.hail.expr.ir.TableKeyByAndAggregate.execute(TableIR.scala:2651)
	at is.hail.expr.ir.TableMapGlobals.execute(TableIR.scala:2312)
	at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:1999)
	at is.hail.expr.ir.TableRename.execute(TableIR.scala:2876)
	at is.hail.expr.ir.TableKeyBy.execute(TableIR.scala:1355)
	at is.hail.expr.ir.TableIR.analyzeAndExecute(TableIR.scala:57)
	at is.hail.expr.ir.Interpret$.run(Interpret.scala:868)
	at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:57)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:20)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:67)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:53)
	at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72)
	at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69)
	at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$3(LoweringPass.scala:16)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
	at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$1(LoweringPass.scala:16)
	at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
	at is.hail.expr.ir.lowering.LoweringPass.apply(LoweringPass.scala:14)
	at is.hail.expr.ir.lowering.LoweringPass.apply$(LoweringPass.scala:13)
	at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64)
	at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:15)
	at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:13)
	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
	at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:38)
	at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13)
	at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:47)
	at is.hail.backend.spark.SparkBackend._execute(SparkBackend.scala:381)
	at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:417)
	at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47)
	at is.hail.utils.package$.using(package.scala:638)
	at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17)
	at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:46)
	at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275)
	at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:414)
	at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)
	at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:413)
	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 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:745)
java.lang.NullPointerException: null
	at __C4220Compiled.apply(Emit.scala)
	at is.hail.expr.ir.TableMapRows.$anonfun$execute$43(TableIR.scala:2031)
	at scala.runtime.java8.JFunction1$mcJJ$sp.apply(JFunction1$mcJJ$sp.java:23)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)
	at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:512)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at is.hail.io.RichContextRDDLong$$anon$3.hasNext(RichContextRDDRegionValue.scala:196)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)
	at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:1087)
	at is.hail.utils.richUtils.RichIterator$$anon$1.isValid(RichIterator.scala:30)
	at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
	at is.hail.utils.BufferedAggregatorIterator.next(BufferedAggregatorIterator.scala:41)
	at is.hail.utils.BufferedAggregatorIterator.next(BufferedAggregatorIterator.scala:9)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:494)
	at is.hail.utils.richUtils.RichContextRDD$$anon$1.next(RichContextRDD.scala:77)
	at scala.collection.Iterator$$anon$11.next(Iterator.scala:494)
	at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:194)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
	at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52)
	at org.apache.spark.scheduler.Task.run(Task.scala:131)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Hail version: 0.2.78-b17627756568
Error summary: NullPointerException: null
6

I think I may have found the issue here:

My regex contains an alternative capturing group, which is then used in the annotation even though it does not always exist:

event_split = ht.microexon_interval_identifier.first_match_in(r"(HsaEX\d{7}|putative_microexon_\d{9})(?:_(.*))?")
ht = ht.annotate(event=event_split[0], event_region=event_split[1])

So, it looks like it’s my bug, but of course it would be nice to get a more informative error message or the option to set the missing values to None.