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Error importlib-metadata package

See original GitHub issue

Good day,

I have tried to run cellbender but I am encountering the next error:

Traceback (most recent call last):
  File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/cellbender/bin/cellbender", line 33, in <module>
    sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
  File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/cellbender/bin/cellbender", line 22, in importlib_load_entry_point
    for entry_point in distribution(dist_name).entry_points
  File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/cellbender/lib/python3.7/site-packages/importlib_metadata/", line 988, in distribution
    return Distribution.from_name(distribution_name)
  File "/hpc/pmc_stunnenberg/cruiz/miniconda3/envs/cellbender/lib/python3.7/site-packages/importlib_metadata/", line 566, in from_name
    raise PackageNotFoundError(name)
importlib_metadata.PackageNotFoundError: No package metadata was found for cellbender

I have installed cell bender according to the instructions in a new conda environment. If import the library in python it works but cellbender does not find it. I have installed importlib-metadata via pip and conda and still do not get it to work.

These are the packages in the conda env

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alabaster                 0.7.12                   pypi_0    pypi
anndata                   0.8.0                    pypi_0    pypi
aom                       3.5.0                h27087fc_0    conda-forge
babel                     2.10.3                   pypi_0    pypi
blas                      1.0                         mkl    anaconda
blosc                     1.21.0               h4ff587b_1    anaconda
brotlipy                  0.7.0           py37h540881e_1004    conda-forge
bzip2                     1.0.8                h7b6447c_0    anaconda
c-ares                    1.18.1               h7f8727e_0    anaconda
ca-certificates           2022.9.24            ha878542_0    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py37h43b0acd_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
cryptography              38.0.2           py37h5994e8b_1    conda-forge
cycler                    0.11.0                   pypi_0    pypi
docutils                  0.17.1                   pypi_0    pypi
expat                     2.5.0                h27087fc_0    conda-forge
ffmpeg                    5.1.2           gpl_hc51e5dc_103    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.1               hc2a2eb6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0                   pypi_0    pypi
freetype                  2.12.1               hca18f0e_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
h5py                      3.7.0                    pypi_0    pypi
hdf5                      1.12.1          nompi_h4df4325_104    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        5.0.0                    pypi_0    pypi
intel-openmp              2021.4.0          h06a4308_3561    anaconda
jinja2                    3.1.2                    pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   h166bdaf_2    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.19.3               h08a2579_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.13.1               h6ed2654_0    conda-forge
ld_impl_linux-64          2.39                 hc81fddc_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libcurl                   7.86.0               h2283fc2_0    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libdrm                    2.4.113              h166bdaf_0    conda-forge
libedit                   3.1.20210910         h7f8727e_0    anaconda
libev                     4.33                 h7f8727e_1    anaconda
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            11.2.0               h00389a5_1    anaconda
libgfortran5              11.2.0               h1234567_1    anaconda
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
libnghttp2                1.47.0               hff17c54_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libpciaccess              0.16                 h516909a_0    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
libsqlite                 3.39.4               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtasn1                  4.19.0               h166bdaf_0    conda-forge
libtiff                   4.4.0                h55922b4_4    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libva                     2.16.0               h166bdaf_0    conda-forge
libvpx                    1.11.0               h9c3ff4c_3    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.3               h7463322_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
lz4-c                     1.9.3                h295c915_1    anaconda
lzo                       2.10                 h7b6447c_2    anaconda
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.5.3                    pypi_0    pypi
mkl                       2021.4.0           h06a4308_640    anaconda
mkl-service               2.4.0            py37h7f8727e_0    anaconda
mkl_fft                   1.3.1            py37hd3c417c_0    anaconda
mkl_random                1.2.2            py37h51133e4_0    anaconda
mock                      4.0.3              pyhd3eb1b0_0    anaconda
natsort                   8.2.0                    pypi_0    pypi
ncurses                   6.3                  h27087fc_1    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
numexpr                   2.8.3            py37h807cd23_0    anaconda
numpy                     1.21.5           py37h6c91a56_3    anaconda
numpy-base                1.21.5           py37ha15fc14_3    anaconda
openh264                  2.3.1                h27087fc_1    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openssl                   3.0.5                h166bdaf_2    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
packaging                 21.3               pyhd3eb1b0_0    anaconda
pandas                    1.3.5                    pypi_0    pypi
pillow                    9.2.0            py37h850a105_2    conda-forge
pip                       22.3               pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0                   pypi_0    pypi
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.4              pyhd3eb1b0_0    anaconda
pyro-api                  0.1.2                    pypi_0    pypi
pyro-ppl                  1.8.2                    pypi_0    pypi
pysocks                   1.7.1            py37h89c1867_5    conda-forge
pytables                  3.7.0            py37h9da3b7f_0    anaconda
python                    3.7.12          hf930737_100_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.7                     2_cp37m    conda-forge
pytorch                   1.13.0              py3.7_cpu_0    pytorch
pytorch-mutex             1.0                         cpu    pytorch
pytz                      2022.5                   pypi_0    pypi
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
scikit-learn              1.0.2                    pypi_0    pypi
scipy                     1.7.3                    pypi_0    pypi
setuptools                65.5.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyhd3eb1b0_1    anaconda
snowballstemmer           2.2.0                    pypi_0    pypi
sphinx                    5.3.0                    pypi_0    pypi
sphinx-argparse           0.3.2                    pypi_0    pypi
sphinx-autodoc-typehints  1.19.4                   pypi_0    pypi
sphinx-rtd-theme          1.0.0                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-programoutput 0.17                     pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.5                    pypi_0    pypi
sqlite                    3.39.4               h4ff8645_0    conda-forge
svt-av1                   1.3.0                h27087fc_0    conda-forge
threadpoolctl             3.1.0                    pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
torchvision               0.14.0                 py37_cpu    pytorch
tqdm                      4.64.1                   pypi_0    pypi
typing_extensions         4.4.0              pyha770c72_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                ha4553b6_0    anaconda

What do you think the problem is?

Thanks in advance!

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:6 (4 by maintainers)

github_iconTop GitHub Comments

ccruizmcommented, Nov 1, 2022

Thanks for all the help @sjfleming ! I could make it work 😃

sjflemingcommented, Oct 31, 2022

As for the docker image on HPC that runs singularity…

Seems like you might be able to do this

singularity build /path/to/downloaded/image/img.simg docker://

and then you can do

singularity exec /path/to/downloaded/image/img.simg ...

(thanks to @mark-chaffin)

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