Hi,
I’m getting an AssertionError in a script I’m running at the step where I’m trying to export some information to a txt file. The script I’m running is here: https://github.com/broadinstitute/gnomad-mitochondria/blob/resources/gnomad_mitochondria/pipeline/add_annotations.py. Would you be able to help interpret this error?
INFO (add annotations 215): Writing sample annotations…
Traceback (most recent call last):
File “/tmp/da8ca10faa85417c9183eab7b9a3380b/add_annotations.py”, line 320, in
main(args)
File “/tmp/da8ca10faa85417c9183eab7b9a3380b/add_annotations.py”, line 218, in main
sample_ht.group_by(sample_ht.hap).aggregate(n=hl.agg.count()).export(
File “”, line 2, in export
File “/opt/conda/default/lib/python3.10/site-packages/hail/typecheck/check.py”, line 584, in wrapper
return original_func(*args, **kwargs)
File “/opt/conda/default/lib/python3.10/site-packages/hail/table.py”, line 1152, in export
Env.backend().execute(
File “/opt/conda/default/lib/python3.10/site-packages/hail/backend/py4j_backend.py”, line 82, in execute
raise e.maybe_user_error(ir) from None
File “/opt/conda/default/lib/python3.10/site-packages/hail/backend/py4j_backend.py”, line 76, in execute
result_tuple = self._jbackend.executeEncode(jir, stream_codec, timed)
File “/usr/lib/spark/python/lib/py4j-0.10.9.5-src.zip/py4j/java_gateway.py”, line 1321, in call
File “/opt/conda/default/lib/python3.10/site-packages/hail/backend/py4j_backend.py”, line 35, in deco
raise fatal_error_from_java_error_triplet(deepest, full, error_id) from None
hail.utils.java.FatalError: AssertionError: assertion failed
Java stack trace:
java.lang.AssertionError: assertion failed
at scala.Predef$.assert(Predef.scala:208)
at is.hail.expr.ir.TableReader.toExecuteIntermediate(TableIR.scala:485)
at is.hail.expr.ir.TableRead.execute(TableIR.scala:1670)
at is.hail.expr.ir.TableIR.analyzeAndExecute(TableIR.scala:61)
at is.hail.expr.ir.Interpret$.run(Interpret.scala:857)
at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:59)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:20)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:58)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:63)
at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:67)
at is.hail.expr.ir.lowering.LoweringPass.$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$.apply(LoweringPass.scala:62)
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:22)
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:20)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:20)
at is.hail.expr.ir.lowering.EvalRelationalLets$.execute$1(EvalRelationalLets.scala:10)
at is.hail.expr.ir.lowering.EvalRelationalLets$.lower$1(EvalRelationalLets.scala:18)
at is.hail.expr.ir.lowering.EvalRelationalLets$.apply(EvalRelationalLets.scala:32)
at is.hail.expr.ir.lowering.EvalRelationalLetsPass.transform(LoweringPass.scala:147)
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.EvalRelationalLetsPass.apply(LoweringPass.scala:141)
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:22)
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:20)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:20)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:50)
at is.hail.backend.spark.SparkBackend._execute(SparkBackend.scala:462)
at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:498)
at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:75)
at is.hail.utils.package$.using(package.scala:635)
at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:75)
at is.hail.utils.package$.using(package.scala:635)
at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17)
at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:63)
at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:350)
at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:495)
at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)
at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:494)
at jdk.internal.reflect.GeneratedMethodAccessor104.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
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.ClientServerConnection.waitForCommands(ClientServerConnection.java:182)
at py4j.ClientServerConnection.run(ClientServerConnection.java:106)
at java.base/java.lang.Thread.run(Thread.java:829)
Hail version: 0.2.120-f00f916faf78
Error summary: AssertionError: assertion failed