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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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error experienced in tutorial #89

Closed chakitarora closed 4 months ago

chakitarora commented 4 months ago

Hi,

i was following the quick_tutorial (5xFAD_paper) to understand the basic pipeline before using it onto my project and i get this error when i execute 'pyWGCNA_5xFAD.findModules()'

Screenshot 2024-02-09 at 16 13 22

. Can you help me with this? Thanks.

SystemExit Traceback (most recent call last) Input In [3], in <cell line: 1>() ----> 1 pyWGCNA_5xFAD.findModules()

File ~/.conda/envs/Py3.10/lib/python3.10/site-packages/PyWGCNA/wgcna.py:300, in WGCNA.findModules(self, **kwargs) 297 self.datExpr.var['dynamicColors'] = WGCNA.labels2colors(labels=dynamicMods) 299 # Calculate eigengenes --> 300 MEList = WGCNA.moduleEigengenes(expr=self.datExpr.to_df(), colors=self.datExpr.var['dynamicColors']) 302 self.MEs = MEList['eigengenes'] 303 if 'MEgrey' in self.MEs.columns:

File ~/.conda/envs/Py3.10/lib/python3.10/site-packages/PyWGCNA/wgcna.py:2036, in WGCNA.moduleEigengenes(expr, colors, impute, nPC, align, excludeGrey, grey, subHubs, softPower, scaleVar, trapErrors) 2034 if not check: 2035 if not trapErrors: -> 2036 sys.exit("Error!") 2037 print(" ..ME calculation of module", modulename, "failed with the following error:", flush=True) 2038 print(" ", pc, " ..the offending module has been removed.", flush=True)

SystemExit: Error!

chakitarora commented 4 months ago

Dependencies of PyWGCNA:

Required | Installed

pandas>=1.4.4 | 2.0.3 numpy==1.23.2 | 1.23.2 scipy>=1.9.1 | 1.11.1 scikit-learn>=1.2.2 | 1.3.0 statsmodels>=0.13.5 | 0.14.0 matplotlib>=3.5.2 | 3.5.2 seaborn>=0.11.2 | 0.12.2 biomart>=0.9.2 | 0.9.2 gseapy>=1.0.1 | 1.0.5 pyvis>=0.3.1 | 0.3.2 setuptools>=67.4.0 | 68.0.0 reactome2py>=3.0.0 | 3.0.0 anndata>=0.8.0 | 0.9.2 requests>=2.28.1 | 2.31.0 networkx>=2.8.4 | 3.1 rsrc>=0.1.3 | 0.1.3 psutil>=5.9.0 | 5.9.1

nargesr commented 4 months ago

Hi,

not sure what’s your problem but which version of PyWGCNA do you have? which version of Python do you have? if your PyWGCNA is any version >= 2.0.0, you should have pandas >= 2.0.0

I also updated requirements.txt, so you can check the version of the packages I have.

I would also make sure I use the latest version of the tutorial and data. I would also try making a new environment and doing a fresh install.

chakitarora commented 4 months ago

I have this:

Python 3.9.0 PyWGCNA 1.16.8 pandas 2.0.3

and i am following the latest github tutorial and data (as linked in the .ipynb)

nargesr commented 4 months ago

if you look at the release log you can find out that even though the version of PyWGCNA ==1.16.8 is stable but is not the latest version and it’s not compatible with pandas >= 2.x.x Also if you look at here, you can find out that I have Python 3.10 so not sure if Python 3.9 is the problem or not

First, I would try to update pyWGCNA and double-check the version of packages with requirements.txt and then if you still have the problem, I would try updating python

chakitarora commented 4 months ago

Thanks for the support. Let me follow the steps you suggested and then see if this issue is resolved.

chakitarora commented 4 months ago

Updated PyWGCNA to 2.0.3. Now it works fine. Thanks!