distributed.core - ERROR #28
Comments
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I have the same issue (distributed.protocol.core - CRITICAL - Failed to deserialize AND _concurrent.futures._base.CancelledError), look like tornado package is involved but I have the latest version? |
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Dear, I did some research and the problem potentially resides in the dask.distributed package (see dask/distributed#1830). The author of the dask framework, Matthew Rocklin, advises to downgrade the version of the tornado package to version 4.5. Could you create a virgin (miniconda) environment in the following way and check if the problem persists? For Linux OS: For Windows: If this resolves the issue I'll put the fix in the source code and create a new release of pyscenic. Many thanks. Kindest regards, |
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Hi , thanks for the quick answear. I downgraded tornado to 4.5 but now I get another error with tornado: tornado.application - ERROR - Exception in callback functools.partial(<function wrap..null_wrapper at 0x2b6d1ffb3598>, |
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Dear Hicham, I tried to reproduce the problem using a fresh installation of pyscenic (version 0.8.16) in a virgin miniconda environment (on a Linux RedHat distribution running on a dual Intel Xeon E5-2680 v3 machine). I installed the latest version of tornado (5.1.1) and ran grnboost from the command line. I failed to get this error message. This is my list of packages installed: Anyhow, this problem is related to the GRNBoost2 step of pySCENIC which is provided through the arboreto package. This issue is already registered there: https://github.com/tmoerman/arboreto/issues/12 . Kindest regards, |
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Dear Bram, arboreto 0.1.5 import pandas as pd I will open an issue on arboreto github, thanks again! Hicham |
Hi Bram, |
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I also have this issue. Has anyone found a solution to it? Updated: |
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Hi, I ended up using a hybrid execution of pySCENIC and SCENIC R where
GRNBoost2 is the only part run through python.
My python modules:
aniso8601==4.0.1
annoy==1.15.1
arboreto==0.1.5
arff==0.9
asn1crypto==0.24.0
attrs==19.1.0
backcall==0.1.0
backports-abc==0.5
backports.shutil-get-terminal-size==1.0.0
bcrypt==3.1.4
biopython==1.72
bitstring==3.1.5
bleach==2.1.3
blist==1.3.6
boltons==19.1.0
CellPhoneDB==1.1.0
certifi==2018.11.29
cffi==1.11.5
chardet==3.0.4
click==6.7
cloudpickle==0.8.1
cryptography==2.3
cycler==0.10.0
Cython==0.29
cytoolz==0.9.0.1
dask==1.0.0
deap==1.2.2
decorator==4.4.0
dill==0.2.9
distributed==1.26.1
ecdsa==0.13
entrypoints==0.2.3
Flask==1.0.2
Flask-RESTful==0.3.6
Flask-Testing==0.7.1
frozendict==1.2
funcsigs==1.0.2
gnureadline==6.3.8
h5py==2.9.0
HeapDict==1.0.0
html5lib==1.0.1
idna==2.7
interlap==0.2.6
ipykernel==4.8.2
ipython==6.4.0
ipython-genutils==0.2.0
ipywidgets==7.2.1
itsdangerous==1.1.0
jedi==0.12.1
Jinja2==2.10
jsonschema==2.6.0
jupyter-client==5.2.3
jupyter-core==4.4.0
kiwisolver==1.0.1
llvmlite==0.26.0
lockfile==0.12.2
loompy==2.0.2
louvain==0.6.1
MarkupSafe==1.1.0
matplotlib==3.0.2
mistune==0.8.3
mock==2.0.0
mpmath==1.0.0
msgpack==0.5.6
multiprocessing-on-dill==3.5.0a4
nbconvert==5.3.1
nbformat==4.4.0
netaddr==0.7.19
netifaces==0.10.7
networkx==2.2
nose==1.3.7
notebook==5.5.0
numba==0.41.0
numpy==1.16.0
pandas==0.23.4
pandocfilters==1.4.2
paramiko==2.4.1
parso==0.3.1
path.py==11.0.1
pathlib2==2.3.2
paycheck==1.0.2
pbr==4.1.0
pexpect==4.6.0
pickleshare==0.7.4
Pillow==5.3.0
prompt-toolkit==1.0.15
psutil==5.4.6
ptyprocess==0.6.0
pyarrow==0.11.1
pyasn1==0.4.3
pycparser==2.18
Pygments==2.2.0
PyNaCl==1.2.1
pyparsing==2.3.1
pyscenic==0.9.7
python-dateutil==2.7.5
python-igraph==0.7.1.post6
pytz==2018.7
PyWavelets==1.0.1
PyYAML==3.13
pyzmq==17.1.0
requests==2.19.1
scikit-image==0.14.2
scikit-learn==0.19.2
scipy==1.2.1
scrublet==0.2
seaborn==0.9.0
Send2Trash==1.5.0
simplegeneric==0.8.1
singledispatch==3.4.0.3
six==1.11.0
sortedcontainers==2.1.0
SQLAlchemy==1.2.14
sympy==1.2
tblib==1.3.2
terminado==0.8.1
testpath==0.3.1
toolz==0.9.0
tornado==5.1.1
tqdm==4.31.1
traitlets==4.3.2
typing==3.6.6
umap==0.1.1
umap-learn==0.3.2
urllib3==1.23
virtualenv==16.0.0
wcwidth==0.1.7
webencodings==0.5.1
Werkzeug==0.14.1
widgetsnbextension==3.2.1
zict==0.1.4
the code for GRNBoost2 python run :
#Author: Hicham Affia - CHU Sainte Justine research center
import os
from distributed import LocalCluster, Client
if __name__ == '__main__':
local_cluster = LocalCluster(n_workers=30,memory_limit=4e9)
custom_client = Client(local_cluster)
#Trick to get the ip adress of the client (custom_client_name)
custom_client_str=str(custom_client)
custom_client_str=custom_client_str.split("'")
custom_client_str_2=custom_client_str[1].split("//")
custom_client_name=custom_client_str_2[1]
command_line="pyscenic grnboost -o grnboost2_output_sample_DGE.csv
--num_workers 30 --client_or_address "+custom_client_name+"
~/path_to_DGE.tsv ~/path_to_TFs_file.tsv"
os.system(command_line)
print("GRNBOOST DONE")
quit("yes")
Hope it helps!
Best,
Hicham
Le mer. 7 juil. 2021 à 07:30, Ionelia ***@***.***> a écrit :
… I also have this issue. Has anyone found a solution to it?
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Hicham Affia, MSc
Bio-informaticien
Laboratoire de génétique cardiovasculaire du Dr Andelfinger
CHU Sainte Justine
Centre de Recherche, 5.17.000
3175 chemin de la Côte-Sainte-Catherine, Montréal, Québec, H3T 1C5
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How could I resolve this issue?
Any suggestion helps..
Thank you very much.
EL
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