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AnantharamanLab / VIBRANT

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ModuleNotFoundError: No module named 'sklearn' #87

Open lynnetea opened 6 months ago

lynnetea commented 6 months ago

Hello, I have been trying to get VIBRANT up and running for a while but keep having issues. I tried to run: VIBRANT_run.py -i mixed_example.fasta

Result was: Traceback (most recent call last): File "/opt/homebrew/anaconda3/envs/VIBRANT/bin/VIBRANT_run.py", line 29, in import sklearn ModuleNotFoundError: No module named 'sklearn

conda list returns:

Name Version Build Channel

biopython 1.81 py311h05b510d_1 conda-forge bottleneck 1.3.5 py311ha0d4635_0 anaconda brotli 1.1.0 hb547adb_1 conda-forge brotli-bin 1.1.0 hb547adb_1 conda-forge bzip2 1.0.8 h93a5062_5 conda-forge ca-certificates 2023.11.17 hf0a4a13_0 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge contourpy 1.2.0 py311hd03642b_0 conda-forge coreutils 9.4 hb547adb_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.7 pypi_0 pypi fonttools 4.47.0 py311h05b510d_0 conda-forge freetype 2.12.1 hadb7bae_2 conda-forge gettext 0.21.1 h0186832_0 conda-forge gzip 1.12 h5eb16cf_0 https://anaconda.org/conda-forge/gzip/1.12/download hmmer 3.4 h7133b54_0 https://anaconda.org/bioconda/hmmer/3.4/download joblib 1.3.2 pypi_0 pypi kiwisolver 1.4.5 py311he4fd1f5_1 conda-forge lcms2 2.16 ha0e7c42_0 conda-forge lerc 4.0.0 h9a09cb3_0 conda-forge libblas 3.9.0 20_osxarm64_openblas conda-forge libbrotlicommon 1.1.0 hb547adb_1 conda-forge libbrotlidec 1.1.0 hb547adb_1 conda-forge libbrotlienc 1.1.0 hb547adb_1 conda-forge libcblas 3.9.0 20_osxarm64_openblas conda-forge libcxx 16.0.6 h4653b0c_0 conda-forge libdeflate 1.19 hb547adb_0 conda-forge libexpat 2.5.0 hb7217d7_1 conda-forge libffi 3.4.2 h3422bc3_5 conda-forge libgfortran 5.0.0 13_2_0_hd922786_1 conda-forge libgfortran5 13.2.0 hf226fd6_1 conda-forge libiconv 1.17 h0d3ecfb_2 conda-forge libidn2 2.3.4 h1a8c8d9_0 conda-forge libjpeg-turbo 3.0.0 hb547adb_1 conda-forge liblapack 3.9.0 20_osxarm64_openblas conda-forge libopenblas 0.3.25 openmp_h6c19121_0 conda-forge libpng 1.6.39 h76d750c_0 conda-forge libsqlite 3.44.2 h091b4b1_0 conda-forge libtiff 4.6.0 ha8a6c65_2 conda-forge libunistring 0.9.10 h3422bc3_0 conda-forge libwebp-base 1.3.2 hb547adb_0 conda-forge libxcb 1.15 hf346824_0 conda-forge libzlib 1.2.13 h53f4e23_5 conda-forge llvm-openmp 17.0.6 hcd81f8e_0 conda-forge matplotlib 3.8.2 py311ha1ab1f8_0 conda-forge matplotlib-base 3.8.2 py311hfdba5f6_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4 h463b476_2 conda-forge numexpr 2.8.7 py311h6dc990b_0 anaconda numpy 1.26.2 py311h6d074dd_0 conda-forge openjpeg 2.5.0 h4c1507b_3 conda-forge openssl 3.2.0 h0d3ecfb_1 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.1.4 py311h6e08293_0 conda-forge patsy 0.5.4 pyhd8ed1ab_0 conda-forge pillow 10.1.0 py311hb9c5795_0 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge prodigal 2.6.3 h2413b67_6 https://anaconda.org/bioconda/prodigal/2.6.3/download pthread-stubs 0.4 h27ca646_1001 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge python 3.11.7 hdf0ec26_0_cpython conda-forge python-dateutil 2.8.2 pyhd3eb1b0_0 anaconda python-tzdata 2023.3 pyhd3eb1b0_0 anaconda python_abi 3.11 4_cp311 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge readline 8.2 h92ec313_1 conda-forge scikit-learn 0.21.3 py37h27c97d8_0 https://anaconda.org/anaconda/scikit-learn/0.21.3/download scipy 1.11.4 py311h2b215a9_0 conda-forge seaborn 0.13.0 hd8ed1ab_0 conda-forge seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge setuptools 68.2.2 pyhd8ed1ab_0 conda-forge six 1.16.0 pyhd3eb1b0_1 anaconda sklearn 0.0 py36hc0b3020_0 https://anaconda.org/jrybka/sklearn/0.0/download statsmodels 0.14.1 py311h9ea6feb_0 conda-forge threadpoolctl 3.2.0 pypi_0 pypi tk 8.6.13 h5083fa2_1 conda-forge tornado 6.3.3 py311heffc1b2_1 conda-forge tzdata 2023c h71feb2d_0 conda-forge vibrant 1.2.0 0 bioconda wget 1.20.3 h470526e_1 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.11 hb547adb_0 conda-forge xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge xz 5.2.6 h57fd34a_0 conda-forge zlib 1.2.13 h53f4e23_5 conda-forge zstd 1.5.5 h4f39d0f_0 conda-forge

Above, you can see the scikit-learn version is 0.21.2 as required in the set up instructions. Any help would be greatly appreciated. I have been trying to get this successfully installed for the past three days :(

KrisKieft commented 5 months ago

Sorry I'm actually not sure why this is happening. Maybe try to git clone the repo and run it from there rather than via the conda install. Then have a conda env with these packages activated.