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patrickwest / EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
MIT License
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ModuleNotFoundError: No module named 'sklearn.svm.classes' #23

Open Sung-hub opened 3 months ago

Sung-hub commented 3 months ago

I was trying to use EukRep and got an error message below: $ EukRep -i LIB204280.asm.p_ctg.fasta -o Euk_contigs.fa Traceback (most recent call last): File "/home/sung.shin/.local/bin/EukRep", line 17, in EukRep.main(args) File "/home/sung.shin/.local/lib/python3.8/site-packages/EukRep/EukRep.py", line 37, in main model = pickle.load(args.model) ModuleNotFoundError: No module named 'sklearn.svm.classes'

I installed the scikit-learn version that was used to create the pickle as the solution showed: $ python

from sklearn import svm from sklearn import datasets clf = svm.SVC() X, y= datasets.load_iris(return_X_y=True) clf.fit(X, y) SVC() import pickle s = pickle.dumps(clf) clf2 = pickle.loads(s) clf2.predict(X[0:1]) array([0]) y[0] 0 from joblib import dump, load dump(clf, 'filename.joblib') ['filename.joblib'] clf = load('filename.joblib')

However, I still got same error message when I tried again:

$ EukRep -i ~/LIB204280/LIB204280.asm.p_ctg.fasta -o ~/LIB204280/Euk_contigs.fa --prokarya ~/LIB204280/Prok_contigs.fa Traceback (most recent call last): File "/home/sung.shin/.local/bin/EukRep", line 17, in EukRep.main(args) File "/home/sung.shin/.local/lib/python3.8/site-packages/EukRep/EukRep.py", line 37, in main model = pickle.load(args.model) ModuleNotFoundError: No module named 'sklearn.svm.classes'

Could you give me some advice?

Sung-hub commented 2 months ago

It was fixed by using singularity as container. $ singularity exec https://depot.galaxyproject.org/singularity/eukrep%3A0.6.7--pyh5e36f6f_2 EukRep