I am having an issue with ld_prune() specifically it seems to be crashing spark. I built in conda using:
conda create -n hail -y gcc_linux-64 hail jupyter firefox
Full environment at the bottom. Builds and runs successfully, Spark UI loads. imports vcf and can do the tutorials, as well as pc_relate() and hwe_normalized_pca()
NAME=“Red Hat Enterprise Linux Server”
VERSION=“7.7 (Maipo)”
Trace:
2020-08-21 18:46:29 Hail: INFO: ld_prune: running local pruning stage with max queue size of 43409 variants
2020-08-21 18:46:36 Hail: INFO: wrote table with 3788 rows in 63 partitions to file:/tmp/hail.cl1aQvYEBsuQ/YbNU3earUV
2020-08-21 18:48:13 Hail: INFO: Wrote all 2 blocks of 3788 x 5981 matrix with block size 4096.
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/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 "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 985, in send_command
response = connection.send_command(command)
File "/data/butlerr/miniconda3/envs/hail/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
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:46460)
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-16-70e0fea94bba>", line 3, in <module>
pruned = hl.ld_prune(kin.GT, r2=0.2, bp_window_size=100000)
File "<decorator-gen-1567>", line 2, in ld_prune
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/statgen.py", line 3429, in ld_prune
entries.i, entries.j, keep=False, tie_breaker=tie_breaker, keyed=False)
File "<decorator-gen-1359>", line 2, in maximal_independent_set
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/misc.py", line 149, in maximal_independent_set
edges.write(edges_path)
File "<decorator-gen-1079>", line 2, in write
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/table.py", line 1221, in write
Env.backend().execute(TableWrite(self._tir, TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/backend/backend.py", line 109, in execute
result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1257, in __call__
answer, self.gateway_client, self.target_id, self.name)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/utils/java.py", line 213, in deco
return f(*args, **kwargs)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/protocol.py", line 336, in get_return_value
format(target_id, ".", name))
py4j.protocol.Py4JError: An error occurred while calling o211.executeJSON
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2044, in showtraceback
stb = value._render_traceback_()
AttributeError: 'Py4JError' object has no attribute '_render_traceback_'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:46460)
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-16-70e0fea94bba>", line 3, in <module>
pruned = hl.ld_prune(kin.GT, r2=0.2, bp_window_size=100000)
File "<decorator-gen-1567>", line 2, in ld_prune
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/statgen.py", line 3429, in ld_prune
entries.i, entries.j, keep=False, tie_breaker=tie_breaker, keyed=False)
File "<decorator-gen-1359>", line 2, in maximal_independent_set
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/misc.py", line 149, in maximal_independent_set
edges.write(edges_path)
File "<decorator-gen-1079>", line 2, in write
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/table.py", line 1221, in write
Env.backend().execute(TableWrite(self._tir, TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/backend/backend.py", line 109, in execute
result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1257, in __call__
answer, self.gateway_client, self.target_id, self.name)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/utils/java.py", line 213, in deco
return f(*args, **kwargs)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/protocol.py", line 336, in get_return_value
format(target_id, ".", name))
py4j.protocol.Py4JError: An error occurred while calling o211.executeJSON
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2044, in showtraceback
stb = value._render_traceback_()
AttributeError: 'Py4JError' object has no attribute '_render_traceback_'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
ERROR:py4j.java_gateway:An error occurred while trying to connect to the Java server (127.0.0.1:46460)
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 3343, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-16-70e0fea94bba>", line 3, in <module>
pruned = hl.ld_prune(kin.GT, r2=0.2, bp_window_size=100000)
File "<decorator-gen-1567>", line 2, in ld_prune
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/statgen.py", line 3429, in ld_prune
entries.i, entries.j, keep=False, tie_breaker=tie_breaker, keyed=False)
File "<decorator-gen-1359>", line 2, in maximal_independent_set
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/misc.py", line 149, in maximal_independent_set
edges.write(edges_path)
File "<decorator-gen-1079>", line 2, in write
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py", line 585, in wrapper
return __original_func(*args_, **kwargs_)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/table.py", line 1221, in write
Env.backend().execute(TableWrite(self._tir, TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/backend/backend.py", line 109, in execute
result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1257, in __call__
answer, self.gateway_client, self.target_id, self.name)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/utils/java.py", line 213, in deco
return f(*args, **kwargs)
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/protocol.py", line 336, in get_return_value
format(target_id, ".", name))
py4j.protocol.Py4JError: An error occurred while calling o211.executeJSON
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2044, in showtraceback
stb = value._render_traceback_()
AttributeError: 'Py4JError' object has no attribute '_render_traceback_'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 929, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/py4j/java_gateway.py", line 1067, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
---------------------------------------------------------------------------
Py4JError Traceback (most recent call last)
<ipython-input-16-70e0fea94bba> in <module>
1 # array imputed, multiiallelics already filtered
2 # biallelic_dataset = dataset.filter_rows(hl.len(dataset.alleles) == 2)
----> 3 pruned = hl.ld_prune(kin.GT, r2=0.2, bp_window_size=100000)
4 kin = kin.filter_rows(hl.is_defined(pruned[kin.row_key]))
5 kin.count()
<decorator-gen-1567> in ld_prune(call_expr, r2, bp_window_size, memory_per_core, keep_higher_maf, block_size)
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
583 def wrapper(__original_func, *args, **kwargs):
584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 585 return __original_func(*args_, **kwargs_)
586
587 return wrapper
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/statgen.py in ld_prune(call_expr, r2, bp_window_size, memory_per_core, keep_higher_maf, block_size)
3427
3428 variants_to_remove = hl.maximal_independent_set(
-> 3429 entries.i, entries.j, keep=False, tie_breaker=tie_breaker, keyed=False)
3430
3431 locally_pruned_table = locally_pruned_table.annotate_globals(
<decorator-gen-1359> in maximal_independent_set(i, j, keep, tie_breaker, keyed)
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
583 def wrapper(__original_func, *args, **kwargs):
584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 585 return __original_func(*args_, **kwargs_)
586
587 return wrapper
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/methods/misc.py in maximal_independent_set(i, j, keep, tie_breaker, keyed)
147 edges = t.select(__i=i, __j=j).key_by().select('__i', '__j')
148 edges_path = new_temp_file()
--> 149 edges.write(edges_path)
150 edges = hl.read_table(edges_path)
151
<decorator-gen-1079> in write(self, output, overwrite, stage_locally, _codec_spec)
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs)
583 def wrapper(__original_func, *args, **kwargs):
584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method)
--> 585 return __original_func(*args_, **kwargs_)
586
587 return wrapper
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/table.py in write(self, output, overwrite, stage_locally, _codec_spec)
1219 """
1220
-> 1221 Env.backend().execute(TableWrite(self._tir, TableNativeWriter(output, overwrite, stage_locally, _codec_spec)))
1222
1223 def _show(self, n, width, truncate, types):
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/backend/backend.py in execute(self, ir, timed)
107
108 def execute(self, ir, timed=False):
--> 109 result = json.loads(Env.hc()._jhc.backend().executeJSON(self._to_java_ir(ir)))
110 value = ir.typ._from_json(result['value'])
111 timings = result['timings']
/data/butlerr/miniconda3/envs/hail/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:
/data/butlerr/miniconda3/envs/hail/lib/python3.6/site-packages/hail/utils/java.py in deco(*args, **kwargs)
211 import pyspark
212 try:
--> 213 return f(*args, **kwargs)
214 except py4j.protocol.Py4JJavaError as e:
215 s = e.java_exception.toString()
/data/butlerr/miniconda3/envs/hail/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 o211.executeJSON
Conda env:
# packages in environment at /data/butlerr/miniconda3/envs/hail:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
aiohttp 3.6.2 py36h516909a_0 conda-forge
aiohttp-session 2.7.0 py_0 conda-forge
argon2-cffi 20.1.0 py36h8c4c3a4_1 conda-forge
async-timeout 3.0.1 py_1000 conda-forge
attrs 20.1.0 pyh9f0ad1d_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
binutils_impl_linux-64 2.34 h2122c62_9 conda-forge
binutils_linux-64 2.34 h47ac705_27 conda-forge
bleach 1.4.2 py36_0 bioconda
blinker 1.4 py_1 conda-forge
bokeh 1.2.0 py36_0 conda-forge
brotlipy 0.7.0 py36h8c4c3a4_1000 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
cachetools 2.1.0 py_0 conda-forge
certifi 2020.6.20 py36h9f0ad1d_0 conda-forge
cffi 1.14.1 py36h0ff685e_0 conda-forge
chardet 3.0.4 py36h9f0ad1d_1006 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
cryptography 3.0 py36h45558ae_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
entrypoints 0.3 py36h9f0ad1d_1001 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
firefox 79.0 he1b5a44_1 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.2 he06d7ca_0 conda-forge
gcc_impl_linux-64 9.3.0 ha2fd2e4_15 conda-forge
gcc_linux-64 9.3.0 h44160b2_27 conda-forge
gcsfs 0.2.1 py_0 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
glib 2.65.0 h6f030ca_0 conda-forge
google-auth 1.2.1 py_0 conda-forge
google-auth-oauthlib 0.4.1 py_2 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
hail 0.2.33 py36hf1ae8f4_1 bioconda
html5lib 1.1 pyh9f0ad1d_0 conda-forge
humanize 2.6.0 py_0 conda-forge
hurry-filesize 0.9 pypi_0 pypi
hurry.filesize 0.9 py36_0 bioconda
icu 64.2 he1b5a44_1 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
idna_ssl 1.1.0 py36_1000 conda-forge
importlib-metadata 1.7.0 py36h9f0ad1d_0 conda-forge
importlib_metadata 1.7.0 0 conda-forge
ipykernel 5.3.4 py36h95af2a2_0 conda-forge
ipython 7.16.1 py36h95af2a2_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.17.2 py36h9f0ad1d_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
jpeg 9d h516909a_0 conda-forge
jsonschema 3.2.0 py36h9f0ad1d_1 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 6.1.6 py_0 conda-forge
jupyter_console 6.1.0 py_1 conda-forge
jupyter_core 4.6.3 py36h9f0ad1d_1 conda-forge
kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge
lcms2 2.11 hbd6801e_0 conda-forge
ld_impl_linux-64 2.34 hc38a660_9 conda-forge
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-devel_linux-64 9.3.0 hfd08b2a_15 conda-forge
libgcc-ng 9.3.0 h24d8f2e_15 conda-forge
libgfortran-ng 7.5.0 hdf63c60_15 conda-forge
libgomp 9.3.0 h24d8f2e_15 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 17_openblas conda-forge
libopenblas 0.3.10 pthreads_hb3c22a3_4 conda-forge
libpng 1.6.37 hed695b0_2 conda-forge
libsodium 1.0.18 h516909a_0 conda-forge
libstdcxx-ng 9.3.0 hdf63c60_15 conda-forge
libtiff 4.1.0 hc7e4089_6 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp-base 1.1.0 h516909a_3 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
markupsafe 1.1.1 py36h8c4c3a4_1 conda-forge
mistune 0.8.4 py36h8c4c3a4_1001 conda-forge
multidict 4.7.5 py36h8c4c3a4_1 conda-forge
nbconvert 5.6.1 py36h9f0ad1d_1 conda-forge
nbformat 5.0.7 py_0 conda-forge
ncurses 6.2 he1b5a44_1 conda-forge
nest-asyncio 1.4.0 py_0 conda-forge
notebook 6.1.3 py36h9f0ad1d_0 conda-forge
numpy 1.19.1 py36h3849536_2 conda-forge
oauthlib 3.0.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openjdk 8.0.192 h516909a_1005 conda-forge
openssl 1.1.1g h516909a_1 conda-forge
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandas 1.1.0 py36h831f99a_0 conda-forge
pandoc 2.10.1 h516909a_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parsimonious 0.8.1 py_0 conda-forge
parso 0.7.1 pyh9f0ad1d_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pexpect 4.8.0 py36h9f0ad1d_1 conda-forge
pickleshare 0.7.5 py36h9f0ad1d_1001 conda-forge
pillow 7.2.0 py36h8328e55_1 conda-forge
pip 20.2.2 py_0 conda-forge
prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge
prompt-toolkit 3.0.6 py_0 conda-forge
prompt_toolkit 3.0.6 0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py4j 0.10.7 py_1 conda-forge
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