Error running vds.summarize


#1

Hey folks. I’ve got Hail running in Jupyter on a Dataproc cluster and it’s mostly working! Mostly.

I’ve managed to call import_vcf from a GCS bucket, write a vds, and call variantqc and export_variants on it.

Unfortunately when I call vds.summarize() I get a pretty gross looking error:

<decorator-gen-523> in summarize(self)

/hail/pyhail-hail-is-master-53e9d33.zip/hail/java.pyc in handle_py4j(func, *args, **kwargs)
    110         raise FatalError('%s\n\nJava stack trace:\n%s\n'
    111                          'Hail version: %s\n'
--> 112                          'Error summary: %s' % (deepest, full, Env.hc().version, deepest))
    113     except py4j.protocol.Py4JError as e:
    114         if e.args[0].startswith('An error occurred while calling'):

FatalError: NullPointerException: null

Java stack trace:
java.lang.NullPointerException: null
	at scala.Option.getOrElse(Option.scala:121)
	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:237)
	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: 0.1-53e9d33
Error summary: NullPointerException: null

Any clues on what I’m doing wrong here?


#2

Hi,
We’ve actually already fixed this bug! Your version is from June 4 – upgrading to the latest will solve the problem. The hash of the most recent stable version is stored in a file at gs://hail-common/builds/0.1/latest-hash-spark-2.0.2.txt


#3

Holy wow, not just that it’s already fixed but at the speed of your response. Thanks!