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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
89 stars 18 forks source link

ModuleNotFoundError: No module named 'sklearn.neighbors.kde' #143

Closed samlipworth closed 3 years ago

samlipworth commented 3 years ago

Just installed poppunk on a new conda env i.e.

conda create -n poppunk conda activate poppunk conda install -c bioconda poppunk

No problems with installation but when trying to run..

Get the error:

ModuleNotFoundError: No module named 'sklearn.neighbors.kde'

Can't run poppunk --version either - same issue.

Any idea what's wrong? Previously ran Poppunk on same machine with no issues.

Thanks

johnlees commented 3 years ago

Can you post the results from conda list within your environment?

samlipworth commented 3 years ago

`# packages in environment at /well/bag/users/lipworth/miniconda3/envs/poppunk: #

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge capnproto 0.6.1 hfc679d8_1 conda-forge certifi 2020.12.5 py36h5fab9bb_1 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge decorator 4.4.2 py_0 conda-forge dendropy 4.5.1 pyh3252c3a_0 bioconda expat 2.2.9 he1b5a44_2 conda-forge fontconfig 2.13.1 h736d332_1003 conda-forge freetype 2.10.4 h7ca028e_0 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge glib 2.66.4 hcd2ae1e_1 conda-forge gsl 2.6 he838d99_1 conda-forge gst-plugins-base 1.14.5 h0935bb2_2 conda-forge gstreamer 1.18.2 h3560a44_1 conda-forge hdbscan 0.8.26 py36ha112f06_3 conda-forge icu 68.1 h58526e2_0 conda-forge joblib 1.0.0 pyhd8ed1ab_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge kiwisolver 1.3.1 py36h51d7077_0 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.11 hcbb858e_1 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_1 conda-forge libblas 3.9.0 7_openblas conda-forge libcblas 3.9.0 7_openblas conda-forge libclang 11.0.0 default_ha5c780c_2 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge libgfortran-ng 9.3.0 he4bcb1c_17 conda-forge libgfortran5 9.3.0 he4bcb1c_17 conda-forge libglib 2.66.4 h164308a_1 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 7_openblas conda-forge libllvm10 10.0.1 he513fc3_3 conda-forge libllvm11 11.0.0 he513fc3_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 12.3 h255efa7_3 conda-forge libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.1.0 h36c2ea0_3 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.10 h72842e0_3 conda-forge llvm-openmp 11.0.0 hfc4b9b4_1 conda-forge llvmlite 0.35.0 py36h05121d2_0 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge mash 2.2.2 ha61e061_2 bioconda matplotlib 3.3.3 py36h5fab9bb_0 conda-forge matplotlib-base 3.3.3 py36he12231b_0 conda-forge mkl 2020.4 h726a3e6_304 conda-forge mysql-common 8.0.22 ha770c72_1 conda-forge mysql-libs 8.0.22 h1fd7589_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge networkx 2.5 py_0 conda-forge nspr 4.29 h9c3ff4c_1 conda-forge nss 3.60 hb5efdd6_0 conda-forge numba 0.52.0 py36h284efc9_0 conda-forge numpy 1.19.5 py36h2aa4a07_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openssl 1.1.1i h7f98852_0 conda-forge pandas 1.1.5 py36h284efc9_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pillow 8.1.0 py36h4f9996e_0 conda-forge pip 20.3.3 pyhd8ed1ab_0 conda-forge poppunk 1.1.3 py36_0 bioconda pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py36h5fab9bb_6 conda-forge pyqt-impl 5.12.3 py36h7ec31b9_6 conda-forge pyqt5-sip 4.19.18 py36hc4f0c31_6 conda-forge pyqtchart 5.12 py36h7ec31b9_6 conda-forge pyqtwebengine 5.12.1 py36h7ec31b9_6 conda-forge python 3.6.12 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2020.5 pyhd8ed1ab_0 conda-forge qt 5.12.9 h9d6b050_2 conda-forge rapidnj 2.3.2 hc9558a2_0 bioconda readline 8.0 he28a2e2_2 conda-forge scikit-learn 0.24.0 py36he4fde30_0 conda-forge scipy 1.5.3 py36h9e8f40b_0 conda-forge setuptools 49.6.0 py36h9880bd3_2 conda-forge sharedmem 0.3.6 py_0 bioconda six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge statsmodels 0.12.1 py36ha112f06_1 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py36h1d69622_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge `

johnlees commented 3 years ago

Looks like an old version of PopPUNK, you've got v1.1.3. Can you upgrade to the current version (v2.3.0)? If you delete your environment, easiest way might be to recreate with:

conda create -c bioconda -n poppunk poppunk==2.3.0
conda activate poppunk
samlipworth commented 3 years ago

Yup fixed thanks