Initializing hail with GRCh38 fails

Hello hail team,

I’m running into some issues initializing hail with GRCh38

import hail as hl
hl.init(default_reference='GRCh38')

I hit this issue in a notebook on 0.2.65 and then updated to 0.2.67 and hit it again after restarting a dataproc cluster. The initialization appears to be happening twice and failing.


The full read out is:


FatalError Traceback (most recent call last)
in
1 from gnomad_qc.v3.resources.release import release_sites, release_ht_path
2 import hail as hl
----> 3 hl.init(default_reference=‘GRCh38’)

in init(sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, spark_conf, skip_logging_configuration, local_tmpdir, _optimizer_iterations)

/opt/conda/miniconda3/lib/python3.8/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
575 def wrapper(original_func, *args, **kwargs):
576 args
, kwargs
= check_all(__original_func, args, kwargs, checkers, is_method=is_method)
→ 577 return original_func(*args, **kwargs)
578
579 return wrapper

/opt/conda/miniconda3/lib/python3.8/site-packages/hail/context.py in init(sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, spark_conf, skip_logging_configuration, local_tmpdir, _optimizer_iterations)
244 optimizer_iterations = get_env_or_default(_optimizer_iterations, ‘HAIL_OPTIMIZER_ITERATIONS’, 3)
245
→ 246 backend = SparkBackend(
247 idempotent, sc, spark_conf, app_name, master, local, log,
248 quiet, append, min_block_size, branching_factor, tmpdir, local_tmpdir,

/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/spark_backend.py in init(self, idempotent, sc, spark_conf, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmpdir, local_tmpdir, skip_logging_configuration, optimizer_iterations)
169 self._jbackend, log, True, append, branching_factor, skip_logging_configuration, optimizer_iterations)
170 else:
→ 171 self._jbackend = hail_package.backend.spark.SparkBackend.apply(
172 jsc, app_name, master, local, True, min_block_size, tmpdir, local_tmpdir)
173 self._jhc = hail_package.HailContext.apply(

/usr/lib/spark/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py in call(self, *args)
1302
1303 answer = self.gateway_client.send_command(command)
→ 1304 return_value = get_return_value(
1305 answer, self.gateway_client, self.target_id, self.name)
1306

/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs)
28 raise FatalError(‘Error summary: %s’ % (deepest,), error_id) from None
29 else:
—> 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

FatalError: IllegalArgumentException: requirement failed

Java stack trace:
java.lang.IllegalArgumentException: requirement failed
at scala.Predef$.require(Predef.scala:268)
at is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:215)
at is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
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: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)

Hail version: 0.2.67-a673309b0445
Error summary: IllegalArgumentException: requirement failed

Please let me know if there is anything else I can provide.
Thanks!
Mike

Sorry, please disregard – this is not a hail issue! I was importing from gnomAD resources above and apparently there is something initializing hail within the module.