[BUG] pyscenic grn ValueError: tuple is not allowed for map key #175
Description
Describe the bug
Error when running pyscenic grn. I am using an older version of dask (1.0.0) as previously suggested.
Steps to reproduce the behavior
- Command run when the error occurred:
pyscenic grn -o results/filtered_adjacencies.csv -m grnboost2 --seed 100 --num_workers 24 --cell_id_attribute CellID --gene_attribute Gene data/merged_all_analysed_filtered.loom resources/tfs_list/lambert2018.txt - Error encountered:
Traceback (most recent call last):
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 421, in main
args.func(args)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 74, in find_adjacencies_command
network = method(expression_data=ex_mtx, tf_names=tf_names, verbose=True, client_or_address=client, seed=args.seed)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/arboreto/algo.py", line 39, in grnboost2
return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/arboreto/algo.py", line 120, in diy
graph = create_graph(expression_matrix,
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/arboreto/core.py", line 403, in create_graph
future_tf_matrix = client.scatter(tf_matrix, broadcast=True)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/client.py", line 2062, in scatter
return self.sync(
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/client.py", line 753, in sync
return sync(self.loop, func, *args, **kwargs)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/utils.py", line 331, in sync
six.reraise(*error[0])
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/six.py", line 703, in reraise
raise value
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/utils.py", line 316, in f
result[0] = yield future
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/client.py", line 1911, in _scatter
yield self.scheduler.scatter(
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/core.py", line 739, in send_recv_from_rpc
result = yield send_recv(comm=comm, op=key, **kwargs)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/core.py", line 533, in send_recv
response = yield comm.read(deserializers=deserializers)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/comm/tcp.py", line 217, in read
msg = yield from_frames(
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/comm/utils.py", line 85, in from_frames
res = _from_frames()
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/comm/utils.py", line 70, in _from_frames
return protocol.loads(
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/distributed/protocol/core.py", line 108, in loads
header = msgpack.loads(header, use_list=False, **msgpack_opts)
File "msgpack/_unpacker.pyx", line 195, in msgpack._cmsgpack.unpackb
ValueError: tuple is not allowed for map key
/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}Expected behavior
Expected pyscenic grn to produce the output file: filtered_adjacencies.csv
Please complete the following information:
- pySCENIC version: 0.10.1
- Installation method: Pip
- Run environment: CLI
- OS: Red Hat 4.4.7-23
- Package versions:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
arboreto 0.1.5 pypi_0 pypi
attrs 19.3.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.5 pyh9f0ad1d_0 conda-forge
boltons 20.1.0 pypi_0 pypi
brotlipy 0.7.0 py38h1e0a361_1000 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
certifi 2020.4.5.1 py38h32f6830_0 conda-forge
cffi 1.14.0 py38hd463f26_0 conda-forge
chardet 3.0.4 py38h32f6830_1006 conda-forge
click 7.1.2 pypi_0 pypi
cloudpickle 1.4.1 pypi_0 pypi
cryptography 2.9.2 py38h766eaa4_0 conda-forge
cytoolz 0.10.1 pypi_0 pypi
dask 1.0.0 pypi_0 pypi
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
dill 0.3.1.1 pypi_0 pypi
distributed 1.28.1 pypi_0 pypi
entrypoints 0.3 py38h32f6830_1001 conda-forge
frozendict 1.2 pypi_0 pypi
h5py 2.10.0 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
idna 2.9 py_1 conda-forge
importlib-metadata 1.6.0 py38h32f6830_0 conda-forge
importlib_metadata 1.6.0 0 conda-forge
interlap 0.2.6 pypi_0 pypi
ipykernel 5.2.1 py38h23f93f0_0 conda-forge
ipython 7.14.0 py38h32f6830_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.17.0 py38h32f6830_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.15.1 pypi_0 pypi
json5 0.9.0 py_0 conda-forge
jsonschema 3.2.0 py38h32f6830_1 conda-forge
jupyter_client 6.1.3 py_0 conda-forge
jupyter_core 4.6.3 py38h32f6830_1 conda-forge
jupyterlab 2.1.2 py_0 conda-forge
jupyterlab_server 1.1.4 py_0 conda-forge
ld_impl_linux-64 2.34 h53a641e_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
llvmlite 0.32.1 pypi_0 pypi
loompy 3.0.6 pypi_0 pypi
markupsafe 1.1.1 py38h1e0a361_1 conda-forge
mistune 0.8.4 py38h1e0a361_1001 conda-forge
msgpack 1.0.0 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
nbconvert 5.6.1 py38h32f6830_1 conda-forge
nbformat 5.0.6 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.4 pypi_0 pypi
notebook 6.0.3 py38h32f6830_0 conda-forge
numba 0.49.1 pypi_0 pypi
numpy 1.18.4 pypi_0 pypi
numpy-groupies 0+unknown pypi_0 pypi
openssl 1.1.1g h516909a_0 conda-forge
packaging 20.1 py_0 conda-forge
pandas 0.25.3 pypi_0 pypi
pandoc 2.9.2.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
pexpect 4.8.0 py38h32f6830_1 conda-forge
pickleshare 0.7.5 py38h32f6830_1001 conda-forge
pip 20.1 pyh9f0ad1d_0 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt-toolkit 3.0.5 py_0 conda-forge
psutil 5.7.0 pypi_0 pypi
ptyprocess 0.6.0 py_1001 conda-forge
pyarrow 0.16.0 pypi_0 pypi
pycparser 2.20 py_0 conda-forge
pygments 2.6.1 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrsistent 0.16.0 py38h1e0a361_0 conda-forge
pyscenic 0.10.1 pypi_0 pypi
pysocks 1.7.1 py38h32f6830_1 conda-forge
python 3.8.2 he5300dc_7_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.8 1_cp38 conda-forge
pytz 2020.1 pypi_0 pypi
pyyaml 5.3.1 pypi_0 pypi
pyzmq 19.0.1 py38ha71036d_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.23.0 pyh8c360ce_2 conda-forge
scikit-learn 0.23.0 pypi_0 pypi
scipy 1.4.1 pypi_0 pypi
send2trash 1.5.0 py_0 conda-forge
setuptools 46.4.0 py38h32f6830_0 conda-forge
six 1.14.0 py_1 conda-forge
sortedcontainers 2.1.0 pypi_0 pypi
sqlite 3.30.1 hcee41ef_0 conda-forge
tbb 2020.0.133 pypi_0 pypi
tblib 1.6.0 pypi_0 pypi
terminado 0.8.3 py38h32f6830_1 conda-forge
testpath 0.4.4 py_0 conda-forge
threadpoolctl 2.0.0 pypi_0 pypi
tk 8.6.10 hed695b0_0 conda-forge
toolz 0.10.0 pypi_0 pypi
tornado 6.0.4 py38h1e0a361_1 conda-forge
tqdm 4.46.0 pypi_0 pypi
traitlets 4.3.3 py38h32f6830_1 conda-forge
umap-learn 0.4.3 pypi_0 pypi
urllib3 1.25.9 py_0 conda-forge
wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.34.2 py_1 conda-forge
xz 5.2.5 h516909a_0 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 2.0.0 pypi_0 pypi
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge