ValueError: Output dtype not compatible with inputs.

[ianfd]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

When we tried to compute QC metrics for our dataset we got this error (see title). Produced by the X.eliminate_zeros() call.

We also traced the error back to genes that have only zeros in them, which would remove these columns and thus change the shape of the matrix. When we removed these genes the error vanished and the program ran successfully.

Minimal code sample

sc.pp.calculate_qc_metrics(
raw_data, qc_vars=["mt", "ribo", "hb"], inplace=True, log1p=True
)

Error output

No response

Versions

-----
anndata     0.10.9
scanpy      1.10.3
-----
PIL                 10.4.0
asttokens           NA
charset_normalizer  3.4.0
colorama            0.4.6
comm                0.2.2
cycler              0.12.1
cython_runtime      NA
dateutil            2.9.0
debugpy             1.8.5
decorator           5.1.1
executing           2.1.0
h5py                3.11.0
ipykernel           6.29.5
jedi                0.19.1
joblib              1.4.2
kiwisolver          1.4.7
legacy_api_wrap     NA
llvmlite            0.43.0
matplotlib          3.9.2
matplotlib_inline   0.1.7
mpl_toolkits        NA
natsort             8.4.0
numba               0.60.0
numpy               2.0.2
packaging           24.1
pandas              2.2.3
parso               0.8.4
pickleshare         0.7.5
platformdirs        4.3.6
prompt_toolkit      3.0.47
psutil              6.0.0
pure_eval           0.2.3
pydev_ipython       NA
pydevconsole        NA
pydevd              2.9.5
pydevd_file_utils   NA
pydevd_plugins      NA
pydevd_tracing      NA
pygments            2.18.0
pyparsing           3.1.4
pytz                2024.1
scipy               1.14.1
session_info        1.0.0
six                 1.16.0
sklearn             1.5.2
stack_data          0.6.2
threadpoolctl       3.5.0
tornado             6.4.1
traitlets           5.14.3
vscode              NA
wcwidth             0.2.13
yaml                6.0.2
zmq                 26.2.0
-----
IPython             8.27.0
jupyter_client      8.6.3
jupyter_core        5.7.2
-----
Python 3.12.6 | packaged by conda-forge | (main, Sep 22 2024, 14:16:49) [GCC 13.3.0]
Linux-5.15.0-122-generic-x86_64-with-glibc2.35
-----
Session information updated at 2024-10-30 08:33

[Zethson]

Could you please post the full stacktrace and ideally provide us with a minimal working example to more easily find out what's going wrong? Can you create an artificial AnnData object that has the properties where the function fails? Can you create a subset of your data and then recreate an AnnData object that looks similar and leads to the issue?

LLMs can help you here.

Thanks!