Hello,
I am getting the following error when I run pc_relate on 4k individuals with 100k markers:
ERROR:root:Exception while sending command. (0 + 1) / 4]
Traceback (most recent call last):
File "/home/unix/aburns/.local/lib/python3.9/site-packages/py4j/clientserver.py", line 516, 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 "/home/unix/aburns/.local/lib/python3.9/site-packages/py4j/java_gateway.py", line 1038, in send_command
response = connection.send_command(command)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/py4j/clientserver.py", line 539, in send_command
raise Py4JNetworkError(
py4j.protocol.Py4JNetworkError: Error while sending or receiving
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<decorator-gen-1708>", line 2, in pc_relate
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/typecheck/check.py", line 584, in wrapper
return __original_func(*args_, **kwargs_)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/methods/relatedness/pc_relate.py", line 344, in pc_relate
ht = Table(ir.BlockMatrixToTableApply(g._bmir, pcs._ir, {
File "<decorator-gen-1110>", line 2, in persist
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/typecheck/check.py", line 584, in wrapper
return __original_func(*args_, **kwargs_)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/table.py", line 2127, in persist
return Env.backend().persist_table(self)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/backend/backend.py", line 163, in persist_table
return t.checkpoint(tf.__enter__())
File "<decorator-gen-1100>", line 2, in checkpoint
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/typecheck/check.py", line 584, in wrapper
return __original_func(*args_, **kwargs_)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/table.py", line 1346, in checkpoint
self.write(output=output, overwrite=overwrite, stage_locally=stage_locally, _codec_spec=_codec_spec)
File "<decorator-gen-1102>", line 2, in write
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/typecheck/check.py", line 584, in wrapper
return __original_func(*args_, **kwargs_)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/table.py", line 1392, in write
Env.backend().execute(ir.TableWrite(self._tir, ir.TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/backend/py4j_backend.py", line 76, in execute
result_tuple = self._jbackend.executeEncode(jir, stream_codec, timed)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/py4j/java_gateway.py", line 1321, in __call__
return_value = get_return_value(
File "/home/unix/aburns/.local/lib/python3.9/site-packages/hail/backend/py4j_backend.py", line 25, in deco
return f(*args, **kwargs)
File "/home/unix/aburns/.local/lib/python3.9/site-packages/py4j/protocol.py", line 334, in get_return_value
raise Py4JError(
py4j.protocol.Py4JError: An error occurred while calling o1.executeEncode
I am using Java 8 and Spark 3.3.2. My code is as follows:
pc_rel = hl.pc_relate(d.GT, k=10, min_individual_maf=0.05, statistics='kin')
Any assistance is greatly appreciated!
Cheers,
Angus