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Error importlib-metadata package
See original GitHub issueGood 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/__init__.py", 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/__init__.py", 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:
- Created a year ago
- Comments:6 (4 by maintainers)
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Thanks for all the help @sjfleming ! I could make it work 😃
As for the docker image on HPC that runs singularity…
Seems like you might be able to do this
and then you can do
(thanks to @mark-chaffin)