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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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concoct_refine error #295

Open tangminBio opened 3 years ago

tangminBio commented 3 years ago

Hello, "concoct_refine clustering_gt1000_R.csv original_data_gt1000.csv clustering_gt1000_scg_sort.csv > concoct_ref.out /home/tm/miniconda3/envs/concoct_env/bin/python: symbol lookup error: /home/tm/miniconda3/envs/concoct_env/lib/python3.8/site-packages/../../libmkl_intel_thread.so: undefined symbol: omp_get_num_procs"

I got this error report, but I have the libmkl_intel_thread.so in the directory, and i do not know how to fix the second error "omp_get_num_procs"

could you please help me? Thanks a lot

tangminBio commented 3 years ago

I added the libiomp5.so file and anther error came: /home/tm/miniconda3/envs/concoct_env/lib/python3.8/site-packages/sklearn/decomposition/_pca.py:461: RuntimeWarning: invalid value encountered in true_divide explainedvariance = (S ** 2) / (n_samples - 1) Traceback (most recent call last): File "/home/tm/miniconda3/envs/concoct_env/bin/concoct_refine", line 81, in main(args) File "/home/tm/miniconda3/envs/concoct_env/bin/concoct_refine", line 48, in main assigns = vbgmm.fit(np.copy(transform_k,order='C'), int(NK), args.seed, args.threads) File "c-concoct/vbgmm.pyx", line 19, in vbgmm.fit TypeError: fit() takes exactly 5 positional arguments (4 given)