ModuleNotFoundError: No module named 'sklearn'

[lynnetea]

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]

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.