encounting issues when running DIALOGUE

[SNOL2]

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Hi, thanks for devloping this fantastic framework! I encounted an error when running dl.calculate_multifactor_PMD. Output are detailed below:

Version information

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anndata 0.10.3 pandas 2.1.3 pertpy 0.6.0 scanpy 1.9.6 scipy 1.11.4 session_info 1.0.0

Cython 3.0.6 PIL 10.0.1 absl NA adjustText 0.8 aiohttp 3.9.1 aiosignal 1.3.1 annotated_types 0.6.0 anyio NA arrow 1.3.0 arviz 0.17.0 asttokens NA async_timeout 4.0.3 attr 23.1.0 attrs 23.1.0 babel 2.13.1 backoff 2.2.1 bokeh 3.3.1 brotli 1.1.0 bs4 4.12.2 certifi 2023.11.17 cffi 1.16.0 chardet 5.2.0 charset_normalizer 3.3.2 chex 0.1.7 click 8.1.7 cloudpickle 3.0.0 colorama 0.4.6 comm 0.1.4 contextlib2 NA croniter NA cycler 0.12.1 cython 3.0.6 cython_runtime NA cytoolz 0.12.2 dask 2023.11.0 dateutil 2.8.2 debugpy 1.8.0 decorator 5.1.1 decoupler 1.5.1 deepdiff 6.7.1 defusedxml 0.7.1 dill 0.3.7 docrep 0.3.2 etils 1.6.0 exceptiongroup 1.2.0 executing 2.0.1 fastapi 0.108.0 fastjsonschema NA flax 0.7.5 fqdn NA frozenlist 1.4.0 fsspec 2023.9.2 gmpy2 2.1.2 h5py 3.9.0 idna 3.6 igraph 0.10.4 importlib_metadata NA importlib_resources NA ipykernel 6.26.0 ipywidgets 8.1.1 isoduration NA jax 0.4.23 jaxlib 0.4.23 jaxopt NA jedi 0.19.1 jinja2 3.1.2 joblib 1.3.2 json5 NA jsonpointer 2.4 jsonschema 4.20.0 jsonschema_specifications NA jupyter_events 0.9.0 jupyter_server 2.11.1 jupyterlab_server 2.25.2 kiwisolver 1.4.5 leidenalg 0.9.1 lightning 2.0.9.post0 lightning_cloud 0.5.57 lightning_fabric 2.1.3 lightning_utilities 0.10.0 llvmlite 0.41.1 lxml 4.9.3 lz4 4.3.2 markupsafe 2.1.3 matplotlib 3.7.2 matplotlib_inline 0.1.6 mizani 0.9.3 ml_collections NA ml_dtypes 0.3.1 mpl_toolkits NA mpmath 1.3.0 msgpack 1.0.7 mudata 0.2.3 multidict 6.0.4 multipart 0.0.6 multipledispatch 0.6.0 natsort 8.4.0 nbformat 5.9.2 numba 0.58.1 numexpr 2.8.7 numpy 1.24.4 numpyro 0.13.2 opt_einsum v3.3.0 optax 0.1.7 ordered_set 4.1.0 ott 0.4.4 overrides NA packaging 23.2 parso 0.8.3 patsy 0.5.3 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA platformdirs 4.0.0 plotnine 0.12.4 ply 3.11 prometheus_client NA prompt_toolkit 3.0.41 psutil 5.9.5 ptyprocess 0.7.0 pure_eval 0.2.2 pyarrow 14.0.1 pycparser 2.21 pydantic 2.1.1 pydantic_core 2.4.0 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.17.2 pyomo 6.7.0 pyparsing 3.0.9 pyro 1.8.6 pythonjsonlogger NA pytorch_lightning 2.1.3 pytz 2023.3.post1 referencing NA requests 2.31.0 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rich NA rpds NA scvi 1.0.4 seaborn 0.12.2 send2trash NA six 1.16.0 sklearn 1.3.2 skmisc 0.3.1 sniffio 1.3.0 socks 1.7.1 soupsieve 2.5 sparse 0.14.0 sparsecca 0.3.1 stack_data 0.6.2 starlette 0.32.0.post1 statsmodels 0.14.0 sympy 1.11.1 tblib 3.0.0 texttable 1.7.0 threadpoolctl 3.2.0 tlz 0.12.2 tomli 2.0.1 toolz 0.12.0 torch 2.1.0 torchgen NA torchmetrics 1.2.1 tornado 6.3.3 tqdm 4.66.1 traitlets 5.14.0 tree 0.1.8 typing_extensions NA uri_template NA urllib3 2.0.7 uvicorn 0.25.0 wcwidth 0.2.12 webcolors 1.13 websocket 1.6.4 websockets 12.0 wrapt 1.16.0 xarray 2023.11.0 xarray_einstats 0.6.0 xyzservices 2023.10.1 yaml 6.0.1 yarl 1.9.3 zipp NA zmq 25.1.1 zoneinfo NA zstandard 0.22.0

IPython 8.18.1 jupyter_client 8.6.0 jupyter_core 5.5.0 jupyterlab 4.0.9

Python 3.10.13 | packaged by conda-forge | (main, Oct 26 2023, 18:07:37) [GCC 12.3.0] Linux-5.4.0-150-generic-x86_64-with-glibc2.28

Session information updated at 2024-03-24 21:56

[SNOL2]

Hi, I have fixed this problem, so I will close this issue. Thanks!

[Zethson]

@SNOL2 could you please document here how you fixed your issue?

[SNOL2]

I just removed samples which had unrepresented cell types following the tutorial and it worked. Sorry for this careless mistake.

[Zethson]

No worries! We should ensure that a more informative error is thrown. Thanks!

[SNOL2]

That would be nice!