2019-07-12 12:16:01 Hail: INFO: linear_regression_rows: running on 284 samples for 1 response variable y,
with input variable x, and 1 additional covariate…
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File “/usr/lib/python3.6/site-packages/py4j/java_gateway.py”, line 1159, in send_command
raise Py4JNetworkError(“Answer from Java side is empty”)
py4j.protocol.Py4JNetworkError: Answer from Java side is empty
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/lib/python3.6/site-packages/py4j/java_gateway.py”, line 985, in send_command
response = connection.send_command(command)
File “/usr/lib/python3.6/site-packages/py4j/java_gateway.py”, line 1164, in send_command
“Error while receiving”, e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
Py4JError Traceback (most recent call last)
in
1 gwas = hl.linear_regression_rows(y=mt.pheno.CaffeineConsumption,
2 x=mt.GT.n_alt_alleles(),
----> 3 covariates=[1.0])
</usr/lib/python3.6/site-packages/decorator.py:decorator-gen-1379> in linear_regression_rows(y, x, covariates, block_size, pass_through)
/usr/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
559 def wrapper(original_func, *args, **kwargs):
560 args, kwargs = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
→ 561 return original_func(*args, **kwargs)
562
563 return wrapper
/usr/lib/python3.6/site-packages/hail/methods/statgen.py in linear_regression_rows(y, x, covariates, block_size, pass_through)
435 ht_result = ht_result.annotate(**{f: ht_result[f][0] for f in fields})
436
→ 437 return ht_result.persist()
438
439
</usr/lib/python3.6/site-packages/decorator.py:decorator-gen-945> in persist(self, storage_level)
/usr/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
559 def wrapper(original_func, *args, **kwargs):
560 args, kwargs = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
→ 561 return original_func(*args, **kwargs)
562
563 return wrapper
/usr/lib/python3.6/site-packages/hail/table.py in persist(self, storage_level)
1757 Persisted table.
1758 “”"
→ 1759 return Env.backend().persist_table(self, storage_level)
1760
1761 def unpersist(self) → ‘Table’:
/usr/lib/python3.6/site-packages/hail/backend/backend.py in persist_table(self, t, storage_level)
123
124 def persist_table(self, t, storage_level):
→ 125 return Table._from_java(self._to_java_ir(t._tir).pyPersist(storage_level))
126
127 def unpersist_table(self, t):
/usr/lib/python3.6/site-packages/py4j/java_gateway.py in call(self, *args)
1255 answer = self.gateway_client.send_command(command)
1256 return_value = get_return_value(
→ 1257 answer, self.gateway_client, self.target_id, self.name)
1258
1259 for temp_arg in temp_args:
/usr/lib/python3.6/site-packages/hail/utils/java.py in deco(*args, **kwargs)
226 import pyspark
227 try:
→ 228 return f(*args, **kwargs)
229 except py4j.protocol.Py4JJavaError as e:
230 s = e.java_exception.toString()
/usr/lib/python3.6/site-packages/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
334 raise Py4JError(
335 “An error occurred while calling {0}{1}{2}”.
→ 336 format(target_id, “.”, name))
337 else:
338 type = answer[1]
Py4JError: An error occurred while calling o149.pyPersist