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?