�[A
100%|██████████| 200/200 [00:07<00:00, 26.87epoch/s, loss=828]
Traceback (most recent call last):
File "copyvae_cnv221/bin/copyvae", line 33, in <module>
sys.exit(load_entry_point('copyVAE', 'console_scripts', 'copyvae')())
File "/home/temp_copyvae/copyVAE-main/copyvae/pipeline.py", line 305, in main
run_pipeline(file, cc_genes, bin_size, max_cp, intermediate_dim, latent_dim, batch_size, epochs, number_of_clones)
File "/home/temp_copyvae/copyVAE-main/copyvae/pipeline.py", line 216, in run_pipeline
data.obsm['latent'] = z
File "copyvae_cnv221/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py", line 216, in __setitem__
value = self._validate_value(value, key)
File "copyvae_cnv221/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py", line 279, in _validate_value
return super()._validate_value(val, key)
File "copyvae_cnv221/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py", line 100, in _validate_value
return coerce_array(val, name=name, allow_df=self._allow_df)
File "copyvae_cnv221/lib/python3.9/site-packages/anndata/_core/storage.py", line 104, in coerce_array
raise ValueError(msg) from e
ValueError: Obsm 'latent' needs to be of one of np.ndarray, numpy.ma.core.MaskedArray, scipy.sparse.spmatrix, awkward.Array, h5py.Dataset, zarr.Array, zappy.base.ZappyArray, anndata.experimental.[CSC,CSR]Dataset, dask.array.Array, cupy.ndarray, or cupyx.scipy.sparse.spmatrix, not <class 'tensorflow.python.framework.ops.EagerTensor'>.
(copyvae_cnv221) $ mamba list
# packages in environment at /.conda/envs/copyvae_cnv221:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.1.0 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
array-api-compat 1.10.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
attrs 25.1.0 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cattrs 24.1.2 pypi_0 pypi
certifi 2025.1.31 pypi_0 pypi
charset-normalizer 3.4.1 pypi_0 pypi
cloudpickle 3.1.1 pypi_0 pypi
contourpy 1.3.0 pypi_0 pypi
copyvae 1.0 dev_0 <develop>
cycler 0.12.1 pypi_0 pypi
decorator 5.2.1 pypi_0 pypi
dm-tree 0.1.8 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
flatbuffers 25.2.10 pypi_0 pypi
fonttools 4.56.0 pypi_0 pypi
future 1.0.0 pypi_0 pypi
gast 0.6.0 pypi_0 pypi
get-annotations 0.1.2 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.70.0 pypi_0 pypi
h5py 3.13.0 pypi_0 pypi
idna 3.10 pypi_0 pypi
importlib-metadata 8.6.1 pypi_0 pypi
importlib-resources 6.5.2 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
keras 3.8.0 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
legacy-api-wrap 1.4.1 pypi_0 pypi
libclang 18.1.1 pypi_0 pypi
libffi 3.4.6 h2dba641_0 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsqlite 3.49.1 hee588c1_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvmlite 0.43.0 pypi_0 pypi
markdown 3.7 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.2 pypi_0 pypi
matplotlib 3.9.4 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
ml-dtypes 0.4.1 pypi_0 pypi
namex 0.0.8 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.2.1 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numpy 2.0.2 pypi_0 pypi
openssl 3.4.1 h7b32b05_0 conda-forge
opt-einsum 3.4.0 pypi_0 pypi
optree 0.14.0 pypi_0 pypi
packaging 24.2 pypi_0 pypi
pandas 2.2.3 pypi_0 pypi
patsy 1.0.1 pypi_0 pypi
pillow 11.1.0 pypi_0 pypi
pip 25.0.1 pyh8b19718_0 conda-forge
platformdirs 4.3.6 pypi_0 pypi
protobuf 5.29.3 pypi_0 pypi
pybiomart 0.2.0 pypi_0 pypi
pygments 2.19.1 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pyparsing 3.2.1 pypi_0 pypi
python 3.9.21 h9c0c6dc_1_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2025.1 pypi_0 pypi
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pypi_0 pypi
requests-cache 1.2.1 pypi_0 pypi
rich 13.9.4 pypi_0 pypi
scanpy 1.10.3 pypi_0 pypi
scikit-learn 1.6.1 pypi_0 pypi
scipy 1.13.1 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 75.8.0 pyhff2d567_0 conda-forge
six 1.17.0 pypi_0 pypi
statsmodels 0.14.4 pypi_0 pypi
stdlib-list 0.11.1 pypi_0 pypi
tensorboard 2.18.0 pypi_0 pypi
tensorboard-data-server 0.7.2 pypi_0 pypi
tensorflow 2.18.0 pypi_0 pypi
tensorflow-io-gcs-filesystem 0.37.1 pypi_0 pypi
tensorflow-probability 0.25.0 pypi_0 pypi
termcolor 2.5.0 pypi_0 pypi
tf-keras 2.18.0 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
tqdm 4.67.1 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2025.1 pypi_0 pypi
umap-learn 0.5.7 pypi_0 pypi
url-normalize 1.4.3 pypi_0 pypi
urllib3 2.3.0 pypi_0 pypi
werkzeug 3.1.3 pypi_0 pypi
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 pypi_0 pypi
zipp 3.21.0 pypi_0 pypi
Hi,
I installed the package with python 3.9 (in conda env with pip and no default packages). When I try to run copyvae with default example, it starts but eventually fails with
Here is the package list I have in my env