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theislab / scib-pipeline

Snakemake pipeline that works with the scIB package to benchmark data integration methods.
MIT License
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Generated test data not readable #26

Closed Hrovatin closed 2 years ago

Hrovatin commented 2 years ago

I generated test data but get the bellow error when trying to read it.


---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
    176         try:
--> 177             return func(elem, *args, **kwargs)
    178         except Exception as e:

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_io/h5ad.py in read_group(group)
    526     if encoding_type:
--> 527         EncodingVersions[encoding_type].check(
    528             group.name, group.attrs["encoding-version"]

~/miniconda3/envs/rpy2_3/lib/python3.8/enum.py in __getitem__(cls, name)
    348     def __getitem__(cls, name):
--> 349         return cls._member_map_[name]
    350 

KeyError: 'dict'

During handling of the above exception, another exception occurred:

AnnDataReadError                          Traceback (most recent call last)
<ipython-input-13-949d8123e8d8> in <module>
      1 import scanpy as sc
----> 2 sc.read("/lustre/groups/ml01/code/karin.hrovatin/scib-pipeline/data/adata_norm.h5ad")

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/scanpy/readwrite.py in read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, cache_compression, **kwargs)
    110     filename = Path(filename)  # allow passing strings
    111     if is_valid_filename(filename):
--> 112         return _read(
    113             filename,
    114             backed=backed,

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/scanpy/readwrite.py in _read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, cache_compression, suppress_cache_warning, **kwargs)
    711     if ext in {'h5', 'h5ad'}:
    712         if sheet is None:
--> 713             return read_h5ad(filename, backed=backed)
    714         else:
    715             logg.debug(f'reading sheet {sheet} from file {filename}')

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_io/h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
    419                 d[k] = read_dataframe(f[k])
    420             else:  # Base case
--> 421                 d[k] = read_attribute(f[k])
    422 
    423         d["raw"] = _read_raw(f, as_sparse, rdasp)

~/miniconda3/envs/rpy2_3/lib/python3.8/functools.py in wrapper(*args, **kw)
    873                             '1 positional argument')
    874 
--> 875         return dispatch(args[0].__class__)(*args, **kw)
    876 
    877     funcname = getattr(func, '__name__', 'singledispatch function')

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
    181             else:
    182                 parent = _get_parent(elem)
--> 183                 raise AnnDataReadError(
    184                     f"Above error raised while reading key {elem.name!r} of "
    185                     f"type {type(elem)} from {parent}."

AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.
mumichae commented 2 years ago

Could you also provide a list of package versions of the pipeline environment?

mamba list
pip list

Also, did you create the adata object in the same pipeline environment you want to run in?

Hrovatin commented 2 years ago

Yes, I created in same env. Also, runPP errors out as 2 mean and std (from hvg) are added to adata, which can not be saved due to repeated var cols.

mamba list ``` # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge abseil-cpp 20211102.0 h27087fc_1 conda-forge absl-py 1.0.0 pyhd8ed1ab_0 conda-forge adjusttext 0.7.3 pypi_0 pypi aioeasywebdav 2.4.0 py38h578d9bd_1001 conda-forge aiohttp 3.8.1 py38h0a891b7_1 conda-forge aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge amply 0.1.4 py_0 conda-forge anndata 0.8.0 py38h578d9bd_0 conda-forge anndata2ri 1.0.6 py_0 bioconda appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py38h497a2fe_1 conda-forge arpack 3.7.0 hdefa2d7_2 conda-forge asttokens 2.0.5 pyhd8ed1ab_0 conda-forge async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge atk-1.0 2.36.0 h3371d22_4 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 21.4.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge backports.zoneinfo 0.2.1 py38h497a2fe_4 conda-forge bbknn 1.5.1 py38hbff2b2d_2 bioconda bcrypt 3.2.0 py38h497a2fe_2 conda-forge beautifulsoup4 4.10.0 pyha770c72_0 conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_9 conda-forge bioconductor-batchelor 1.10.0 r41h619a076_1 bioconda bioconductor-beachmat 2.10.0 r41h619a076_1 bioconda bioconductor-biobase 2.54.0 r41h5c21468_1 bioconda bioconductor-biocgenerics 0.40.0 r41hdfd78af_0 bioconda bioconductor-biocneighbors 1.12.0 r41h619a076_1 bioconda bioconductor-biocparallel 1.28.3 r41h619a076_0 bioconda bioconductor-biocsingular 1.10.0 r41h619a076_1 bioconda bioconductor-bluster 1.4.0 r41h619a076_1 bioconda bioconductor-delayedarray 0.20.0 r41h5c21468_1 bioconda bioconductor-delayedmatrixstats 1.16.0 r41hdfd78af_0 bioconda bioconductor-edger 3.36.0 r41h619a076_1 bioconda bioconductor-genomeinfodb 1.30.0 r41hdfd78af_0 bioconda bioconductor-genomeinfodbdata 1.2.7 r41hdfd78af_1 bioconda bioconductor-genomicranges 1.46.1 r41h5c21468_0 bioconda bioconductor-iranges 2.28.0 r41h5c21468_1 bioconda bioconductor-limma 3.50.1 r41h5c21468_0 bioconda bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 bioconda bioconductor-metapod 1.2.0 r41h619a076_1 bioconda bioconductor-residualmatrix 1.4.0 r41hdfd78af_0 bioconda bioconductor-s4vectors 0.32.3 r41h5c21468_0 bioconda bioconductor-scaledmatrix 1.2.0 r41hdfd78af_0 bioconda bioconductor-scater 1.22.0 r41hdfd78af_0 bioconda bioconductor-scran 1.22.1 r41h619a076_0 bioconda bioconductor-scuttle 1.4.0 r41h619a076_1 bioconda bioconductor-singlecellexperiment 1.16.0 r41hdfd78af_0 bioconda bioconductor-sparsematrixstats 1.6.0 r41h619a076_1 bioconda bioconductor-summarizedexperiment 1.24.0 r41hdfd78af_0 bioconda bioconductor-xvector 0.34.0 r41h5c21468_1 bioconda bioconductor-zlibbioc 1.40.0 r41h5c21468_1 bioconda bleach 4.1.0 pyhd8ed1ab_0 conda-forge blinker 1.4 py_1 conda-forge boto3 1.21.32 pyhd8ed1ab_0 conda-forge botocore 1.24.32 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h166bdaf_7 conda-forge brotli-bin 1.0.9 h166bdaf_7 conda-forge brotlipy 0.7.0 py38h0a891b7_1004 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 4.2.4 pyhd8ed1ab_0 conda-forge cairo 1.16.0 ha61ee94_1011 conda-forge certifi 2021.10.8 py38h578d9bd_2 conda-forge cffi 1.15.0 py38h3931269_0 conda-forge charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge chex 0.1.2 pyhd8ed1ab_0 conda-forge click 8.1.2 py38h578d9bd_0 conda-forge coin-or-cbc 2.10.7 h3786ebc_0 conda-forge coin-or-cgl 0.60.3 he7e83c3_2 conda-forge coin-or-clp 1.17.6 h256e9bb_3 conda-forge coin-or-osi 0.108.6 h3b589db_2 conda-forge coin-or-utils 2.11.6 h573740c_0 conda-forge coincbc 2.10.7 0_metapackage conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge commonmark 0.9.1 py_0 conda-forge configargparse 1.5.3 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 36.0.0 py38h9ce1e76_0 curl 7.82.0 h2283fc2_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge datrie 0.8.2 py38h497a2fe_3 conda-forge debugpy 1.5.1 py38h709712a_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dm-tree 0.1.6 py38h56ea1f7_1 conda-forge docrep 0.3.2 pyh44b312d_0 conda-forge docutils 0.18.1 py38h578d9bd_1 conda-forge dropbox 11.29.0 pyhd8ed1ab_0 conda-forge dunamai 1.11.0 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge et_xmlfile 1.0.1 py_1001 conda-forge executing 0.8.3 pyhd8ed1ab_0 conda-forge expat 2.4.8 h27087fc_0 conda-forge fbpca 1.0 pypi_0 pypi filechunkio 1.8 py_2 conda-forge filelock 3.6.0 pyhd8ed1ab_0 conda-forge flax 0.4.1 pyhd8ed1ab_0 conda-forge flit-core 3.7.1 pyhd8ed1ab_0 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 2.13.96 h8e229c2_2 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.31.2 py38h0a891b7_0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozenlist 1.3.0 py38h0a891b7_1 conda-forge fsspec 2022.3.0 pyhd8ed1ab_0 conda-forge ftputil 5.0.3 pyhd8ed1ab_0 conda-forge future 0.18.2 py38h578d9bd_5 conda-forge future-fstrings 1.2.0 pypi_0 pypi gcc_impl_linux-64 10.3.0 hf2f2afa_14 conda-forge gcc_linux-64 10.3.0 hc39de41_9 conda-forge gdk-pixbuf 2.42.8 hff1cb4f_0 conda-forge gdown 4.4.0 pypi_0 pypi geosketch 1.2 pypi_0 pypi get_version 3.5.4 pyhd8ed1ab_0 conda-forge gettext 0.19.8.1 h73d1719_1008 conda-forge gfortran_impl_linux-64 10.3.0 h73f4979_14 conda-forge gfortran_linux-64 10.3.0 hb09a455_9 conda-forge giflib 5.2.1 h36c2ea0_2 conda-forge git 2.35.1 pl5321h04cb727_0 conda-forge gitdb 4.0.9 pyhd8ed1ab_0 conda-forge gitpython 3.1.27 pyhd8ed1ab_0 conda-forge glpk 4.65 h9202a9a_1004 conda-forge gmp 6.2.1 h58526e2_0 conda-forge google-api-core 2.5.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.42.0 pyhd8ed1ab_0 conda-forge google-auth 1.35.0 pyh6c4a22f_0 conda-forge google-auth-httplib2 0.1.0 pyhd8ed1ab_0 conda-forge google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge google-cloud-core 2.2.2 pyhd3eb1b0_0 google-cloud-storage 2.1.0 pyh6c4a22f_0 conda-forge google-crc32c 1.1.2 py38h8838a9a_2 conda-forge google-resumable-media 2.1.0 pyh6c4a22f_0 conda-forge googleapis-common-protos 1.56.0 py38h578d9bd_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 3.0.0 h5abf519_1 conda-forge grpc-cpp 1.44.0 h1021d7f_1 conda-forge grpcio 1.45.0 py38h2e9ca35_0 conda-forge gsl 2.7 he838d99_0 conda-forge gtk2 2.24.33 h90689f9_2 conda-forge gts 0.7.6 h64030ff_2 conda-forge gxx_impl_linux-64 10.3.0 hf2f2afa_14 conda-forge gxx_linux-64 10.3.0 h2593f52_9 conda-forge h5py 3.6.0 nompi_py38hfbb2109_100 conda-forge harfbuzz 4.2.0 hf9f4e7c_1 conda-forge hdf5 1.12.1 nompi_h4df4325_104 conda-forge httplib2 0.20.4 pyhd8ed1ab_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.3 pyhd8ed1ab_0 conda-forge igraph 0.9.9 pypi_0 pypi importlib-metadata 4.11.3 py38h578d9bd_1 conda-forge importlib_metadata 4.11.3 hd8ed1ab_1 conda-forge importlib_resources 5.6.0 pyhd8ed1ab_0 conda-forge iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge intel-openmp 2022.0.1 h06a4308_3633 intervaltree 3.1.0 pypi_0 pypi ipykernel 6.11.0 py38h7f3c49e_2 conda-forge ipython 8.2.0 py38h578d9bd_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.7.0 pyhd8ed1ab_0 conda-forge jax 0.3.4 pyhd8ed1ab_0 conda-forge jaxlib 0.3.0 py38h1302da7_4 conda-forge jbig 2.1 h7f98852_2003 conda-forge jedi 0.18.1 py38h578d9bd_0 conda-forge jinja2 3.1.1 pyhd8ed1ab_0 conda-forge jmespath 1.0.0 pyhd8ed1ab_0 conda-forge joblib 1.1.0 pyhd8ed1ab_0 conda-forge jpeg 9e h7f98852_0 conda-forge jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge jupyter_client 7.2.1 pyhd8ed1ab_0 conda-forge jupyter_core 4.9.2 py38h578d9bd_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_widgets 1.1.0 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.2 py38h43d8883_1 conda-forge krb5 1.19.3 h08a2579_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libblas 3.9.0 13_linux64_mkl conda-forge libbrotlicommon 1.0.9 h166bdaf_7 conda-forge libbrotlidec 1.0.9 h166bdaf_7 conda-forge libbrotlienc 1.0.9 h166bdaf_7 conda-forge libcblas 3.9.0 13_linux64_mkl conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 7.82.0 h2283fc2_0 conda-forge libdeflate 1.10 h7f98852_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 10.3.0 he6cfe16_14 conda-forge libgcc-ng 11.2.0 h1d223b6_14 conda-forge libgd 2.3.3 h18fbbfe_3 conda-forge libgfortran-ng 11.2.0 h69a702a_14 conda-forge libgfortran5 11.2.0 h5c6108e_14 conda-forge libgit2 1.4.2 h4c07d5c_0 conda-forge libglib 2.70.2 h174f98d_4 conda-forge libgomp 11.2.0 h1d223b6_14 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 13_linux64_mkl conda-forge liblapacke 3.9.0 13_linux64_mkl conda-forge libllvm9 9.0.1 default_hc23dcda_7 conda-forge libnghttp2 1.47.0 he49606f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libprotobuf 3.19.4 h780b84a_0 conda-forge librsvg 2.52.5 h0a9e6e8_2 conda-forge libsanitizer 10.3.0 h26c7422_14 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.10.0 ha35d2d1_2 conda-forge libstdcxx-devel_linux-64 10.3.0 he6cfe16_14 conda-forge libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge libtiff 4.3.0 h542a066_3 conda-forge libtool 2.4.6 h9c3ff4c_1008 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp 1.2.2 h3452ae3_0 conda-forge libwebp-base 1.2.2 h7f98852_1 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.9.12 h22db469_2 conda-forge libzlib 1.2.11 h166bdaf_1014 conda-forge llvmlite 0.33.0 py38h4f45e52_1 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge louvain 0.7.1 pypi_0 pypi lz4-c 1.9.3 h9c3ff4c_1 conda-forge make 4.3 hd18ef5c_1 conda-forge markdown 3.3.6 pyhd8ed1ab_0 conda-forge markupsafe 2.1.1 py38h0a891b7_1 conda-forge matplotlib-base 3.5.1 py38hf4fb855_0 conda-forge matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge metis 5.1.0 h58526e2_1006 conda-forge mistune 0.8.4 py38h497a2fe_1005 conda-forge mkl 2022.0.1 h06a4308_117 mpfr 4.1.0 h9202a9a_1 conda-forge msgpack-python 1.0.3 py38h43d8883_1 conda-forge multidict 6.0.2 py38h0a891b7_1 conda-forge multipledispatch 0.6.0 py_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge natsort 8.1.0 pyhd8ed1ab_0 conda-forge nbclient 0.5.13 pyhd8ed1ab_0 conda-forge nbconvert 6.4.5 py38h578d9bd_0 conda-forge nbformat 5.2.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h9c3ff4c_0 conda-forge nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge networkx 2.7.1 pyhd8ed1ab_1 conda-forge ninja 1.10.2 h4bd325d_1 conda-forge notebook 6.4.10 pyha770c72_0 conda-forge numba 0.50.1 py38hcb8c335_1 conda-forge numpy 1.22.3 py38h05e7239_0 conda-forge numpyro 0.9.1 pyhd8ed1ab_0 conda-forge oauth2client 4.1.3 py_0 conda-forge oauthlib 3.2.0 pyhd8ed1ab_0 conda-forge openblas 0.3.18 pthreads_h4748800_0 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openpyxl 3.0.9 pyhd8ed1ab_0 conda-forge openssl 3.0.2 h166bdaf_1 conda-forge opt_einsum 3.3.0 pyhd8ed1ab_1 conda-forge optax 0.1.1 pyhd8ed1ab_0 conda-forge packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.4.2 py38h47df419_0 conda-forge pandoc 2.17.1.1 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge pango 1.50.6 hbd2fdc8_0 conda-forge paramiko 2.10.3 pyhd8ed1ab_0 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pypi_0 pypi typing-extensions 3.10.0.2 hd8ed1ab_0 conda-forge typing_extensions 3.10.0.2 pyha770c72_0 conda-forge tzdata 2022a h191b570_0 conda-forge tzlocal 4.2 py38h578d9bd_0 conda-forge ubiquerg 0.6.1 pyh9f0ad1d_0 conda-forge umap-learn 0.4.6 py38h32f6830_0 conda-forge unicodedata2 14.0.0 py38h497a2fe_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.9 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge werkzeug 2.1.1 pyhd8ed1ab_0 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge widgetsnbextension 3.6.0 py38h578d9bd_0 conda-forge wrapt 1.14.0 py38h0a891b7_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 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-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.7.2 py38h0a891b7_2 conda-forge yte 1.2.0 py38h578d9bd_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zipp 3.8.0 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h166bdaf_1014 conda-forge zstd 1.5.2 ha95c52a_0 conda-forge ```
pip list ``` Package Version ----------------------------- ------------- absl-py 1.0.0 adjustText 0.7.3 aioeasywebdav 2.4.0 aiohttp 3.8.1 aiosignal 1.2.0 amply 0.1.4 anndata 0.8.0 anndata2ri 0.0.0 annoy 1.17.0 appdirs 1.4.4 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 asttokens 2.0.5 async-timeout 4.0.2 attmap 0.13.2 attrs 21.4.0 backcall 0.2.0 backports.functools-lru-cache 1.6.4 backports.zoneinfo 0.2.1 bbknn 1.5.1 bcrypt 3.2.0 beautifulsoup4 4.10.0 bleach 4.1.0 blinker 1.4 boto3 1.21.32 botocore 1.24.32 brotlipy 0.7.0 cached-property 1.5.2 cachetools 4.2.4 certifi 2021.10.8 cffi 1.15.0 charset-normalizer 2.0.12 chex 0.1.2 click 8.1.2 colorama 0.4.4 commonmark 0.9.1 ConfigArgParse 1.5.3 connection-pool 0.0.3 cryptography 36.0.0 cycler 0.10.0 dataclasses 0.8 datrie 0.8.2 debugpy 1.5.1 decorator 4.4.2 defusedxml 0.7.1 Deprecated 1.2.12 dm-tree 0.1.6 docrep 0.3.2 docutils 0.18.1 dropbox 11.29.0 dunamai 1.11.0 entrypoints 0.4 et-xmlfile 1.0.1 executing 0.8.3 fbpca 1.0 filechunkio 1.8 filelock 3.6.0 flatbuffers 2.0 flax 0.4.1 flit_core 3.7.1 fonttools 4.31.2 frozenlist 1.3.0 fsspec 2022.3.0 ftputil 5.0.3 future 0.18.2 future-fstrings 1.2.0 gdown 4.4.0 geosketch 1.2 get_version 3.5.4 gitdb 4.0.9 GitPython 3.1.27 google-api-core 2.5.0 google-api-python-client 2.42.0 google-auth 1.35.0 google-auth-httplib2 0.1.0 google-auth-oauthlib 0.4.6 google-cloud-core 2.2.2 google-cloud-storage 2.1.0 google-crc32c 1.1.2 google-resumable-media 2.1.0 googleapis-common-protos 1.56.0 graphtools 1.5.2 grpcio 1.45.0 h5py 3.6.0 httplib2 0.20.4 idna 3.3 igraph 0.9.9 importlib-metadata 4.11.3 importlib-resources 5.6.0 iniconfig 1.1.1 intervaltree 3.1.0 ipykernel 6.11.0 ipython 8.2.0 ipython-genutils 0.2.0 ipywidgets 7.7.0 jax 0.3.4 jaxlib 0.3.0 jedi 0.18.1 Jinja2 3.1.1 jmespath 1.0.0 joblib 1.0.1 jsonschema 4.4.0 jupyter-client 7.2.1 jupyter-core 4.9.2 jupyterlab-pygments 0.1.2 jupyterlab-widgets 1.1.0 kiwisolver 1.3.1 llvmlite 0.33.0 logmuse 0.2.6 louvain 0.7.1 magic-impute 3.0.0 Markdown 3.3.6 MarkupSafe 2.1.1 matplotlib 3.4.0 matplotlib-inline 0.1.3 mistune 0.8.4 msgpack 1.0.3 multidict 6.0.2 multipledispatch 0.6.0 munkres 1.1.4 natsort 8.1.0 nbclient 0.5.13 nbconvert 6.4.5 nbformat 5.2.0 nest-asyncio 1.5.5 networkx 2.7.1 notebook 6.4.10 numba 0.50.1 numpy 1.22.3 numpyro 0.9.1 oauth2client 4.1.3 oauthlib 3.2.0 openpyxl 3.0.9 opt-einsum 3.3.0 optax 0.1.1 packaging 21.3 pandas 1.4.2 pandocfilters 1.5.0 paramiko 2.10.3 parso 0.8.3 patsy 0.5.2 peppy 0.31.2 pexpect 4.8.0 pickleshare 0.7.5 Pillow 8.1.2 pip 22.0.4 plac 1.3.5 pluggy 1.0.0 ply 3.11 prettytable 3.2.0 prometheus-client 0.13.1 prompt-toolkit 3.0.27 protobuf 3.19.4 psutil 5.9.0 ptyprocess 0.7.0 PuLP 2.6.0 pure-eval 0.2.2 py 1.11.0 pyasn1 0.4.8 pyasn1-modules 0.2.7 pycparser 2.21 pyDeprecate 0.3.1 pydot 1.4.2 Pygments 2.11.2 PyGSP 0.5.1 PyJWT 2.3.0 PyNaCl 1.5.0 pynndescent 0.5.6 pyOpenSSL 22.0.0 pyparsing 2.4.7 pyro-api 0.1.2 pyro-ppl 1.8.1+06911dc pyrsistent 0.18.1 pysftp 0.2.9 PySocks 1.7.1 pytest 7.1.1 python-dateutil 2.8.2 python-igraph 0.9.9 python-irodsclient 1.1.2 pytorch-lightning 1.5.8 pytz 2022.1 pytz-deprecation-shim 0.1.0.post0 pyu2f 0.1.5 PyYAML 6.0 pyzmq 22.3.0 ratelimiter 1.2.0 requests 2.27.1 requests-oauthlib 1.3.1 retry 0.9.2 rich 12.1.0 rpy2 3.4.5 rsa 4.8 s3transfer 0.5.2 scanorama 1.7.2 scanpy 1.9.0 scArches 0.5.1 scib 1.0.1 scikit-learn 0.24.1 scikit-misc 0.1.4 scipy 1.8.0 scprep 1.1.0 scvi-tools 0.15.4 seaborn 0.11.2 Send2Trash 1.8.0 session-info 1.0.0 setuptools 61.3.1 simplegeneric 0.8.1 six 1.16.0 slacker 0.14.0 smart-open 5.2.1 smmap 3.0.5 snakemake 7.3.6 sortedcontainers 2.4.0 soupsieve 2.3.1 stack-data 0.2.0 statsmodels 0.13.2 stdlib-list 0.8.0 stone 3.3.1 stopit 1.1.2 tabulate 0.8.9 tasklogger 1.0.0 tensorboard 2.4.1 tensorboard-plugin-wit 1.8.1 terminado 0.13.3 testpath 0.6.0 texttable 1.6.4 threadpoolctl 2.1.0 tomli 2.0.1 toolz 0.11.2 toposort 1.7 torch 1.11.0 torchmetrics 0.7.3 torchvision 0.12.0 tornado 6.1 tqdm 4.64.0 traitlets 5.1.1 trvaep 0.1.0 typing-extensions 3.10.0.2 tzdata 2022.1 tzlocal 4.2 ubiquerg 0.6.1 umap-learn 0.4.6 unicodedata2 14.0.0 uritemplate 4.1.1 urllib3 1.26.9 veracitools 0.1.3 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 2.1.1 wheel 0.37.1 widgetsnbextension 3.6.0 wrapt 1.12.1 yarl 1.7.2 yte 1.2.0 zipp 3.8.0
mumichae commented 2 years ago

Could this be related? https://github.com/scverse/scanpy/issues/1351

mumichae commented 2 years ago

Also, from what I can see in the stacktrace, you seem to be in the rpy2_3 environment. Does the same thing happen when you read the object in scib-pipeline?

Hrovatin commented 2 years ago

Ah yes, I was doing it from jupyter so it used the wrong R env (the one from where jupyter was started, not the one I was using for the kernel). Solved now. But still odd as i could read other adata objects normally.

mumichae commented 2 years ago

I think there might have been some API changes in anndata so that files written in one version cannot be read in another