pycisTopic
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aertslab
Numba ConstantInferenceError in find_diff_features [BUG]
First, I'd like thank you very much for the great work and package you created! I am trying to run the different steps in the Multiome tutorial (https://scenicplus.readthedocs.io/en/latest/pbmc_multiome_tutorial.html) and am getting stuck at the DAR step.
When I run:
from pycisTopic.diff_features import *
imputed_acc_obj = impute_accessibility(cistopic_obj, selected_cells=None, selected_regions=None, scale_factor=10**6)
normalized_imputed_acc_obj = normalize_scores(imputed_acc_obj, scale_factor=10**4)
variable_regions = find_highly_variable_features(normalized_imputed_acc_obj, plot = False)
markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='highlevel_annotation', var_features=variable_regions, split_pattern = '-')
I get the following error:
2023-09-19 15:30:00,761 cisTopic INFO Imputing region accessibility
2023-09-19 15:30:00,762 cisTopic INFO Impute region accessibility for regions 0-20000
2023-09-19 15:30:00,902 cisTopic INFO Impute region accessibility for regions 20000-40000
2023-09-19 15:30:01,010 cisTopic INFO Impute region accessibility for regions 40000-60000
2023-09-19 15:30:01,132 cisTopic INFO Impute region accessibility for regions 60000-80000
2023-09-19 15:30:01,258 cisTopic INFO Impute region accessibility for regions 80000-100000
2023-09-19 15:30:01,382 cisTopic INFO Impute region accessibility for regions 100000-120000
2023-09-19 15:30:01,464 cisTopic INFO Done!
2023-09-19 15:30:01,465 cisTopic INFO Normalizing imputed data
2023-09-19 15:30:04,534 cisTopic INFO Done!
2023-09-19 15:30:04,535 cisTopic INFO Calculating mean
2023-09-19 15:30:04,704 cisTopic INFO Calculating variance
2023-09-19 15:30:08,025 cisTopic INFO Done!
2023-09-19 15:30:08,495 cisTopic INFO Subsetting data for Carcinoma (653 of 1479)
---------------------------------------------------------------------------
ConstantInferenceError Traceback (most recent call last)
Cell In[29], line 5
3 normalized_imputed_acc_obj = normalize_scores(imputed_acc_obj, scale_factor=10**4)
4 variable_regions = find_highly_variable_features(normalized_imputed_acc_obj, plot = False)
----> 5 markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='highlevel_annotation', var_features=variable_regions, split_pattern = '-')
File ~/opt/anaconda3/envs/spatial/lib/python3.9/site-packages/pycisTopic/diff_features.py:800, in find_diff_features(cistopic_obj, imputed_features_obj, variable, var_features, contrasts, adjpval_thr, log2fc_thr, split_pattern, n_cpu, **kwargs)
798 ray.shutdown()
799 else:
--> 800 markers_list = [
801 markers(
802 subset_imputed_features_obj,
803 barcode_groups[i],
804 contrasts_names[i],
805 adjpval_thr=adjpval_thr,
806 log2fc_thr=log2fc_thr,
807 n_cpu=1,
808 )
809 for i in range(len(contrasts))
810 ]
812 markers_dict = {
813 contrasts_name: marker
814 for contrasts_name, marker in zip(contrasts_names, markers_list)
815 }
817 return markers_dict
File ~/opt/anaconda3/envs/spatial/lib/python3.9/site-packages/pycisTopic/diff_features.py:801, in <listcomp>(.0)
798 ray.shutdown()
799 else:
800 markers_list = [
--> 801 markers(
802 subset_imputed_features_obj,
803 barcode_groups[i],
804 contrasts_names[i],
805 adjpval_thr=adjpval_thr,
806 log2fc_thr=log2fc_thr,
807 n_cpu=1,
808 )
809 for i in range(len(contrasts))
810 ]
812 markers_dict = {
813 contrasts_name: marker
814 for contrasts_name, marker in zip(contrasts_names, markers_list)
815 }
817 return markers_dict
File ~/opt/anaconda3/envs/spatial/lib/python3.9/site-packages/pycisTopic/diff_features.py:884, in markers(input_mat, barcode_group, contrast_name, adjpval_thr, log2fc_thr, n_cpu)
882 bg_mat = mat[:, bg_cells_index].toarray()
883 else:
--> 884 fg_mat = subset_array_second_axis(arr=mat, col_indices=fg_cells_index)
885 bg_mat = subset_array_second_axis(arr=mat, col_indices=bg_cells_index)
887 log.info(f"Computing p-value for {contrast_name}")
File ~/opt/anaconda3/envs/spatial/lib/python3.9/site-packages/numba/core/dispatcher.py:480, in _DispatcherBase._compile_for_args(self, *args, **kws)
476 error_rewrite(e, 'interpreter')
477 except errors.ConstantInferenceError as e:
478 # this is from trying to infer something as constant when it isn't
479 # or isn't supported as a constant
--> 480 error_rewrite(e, 'constant_inference')
481 except Exception as e:
482 if config.SHOW_HELP:
File ~/opt/anaconda3/envs/spatial/lib/python3.9/site-packages/numba/core/dispatcher.py:409, in _DispatcherBase._compile_for_args.<locals>.error_rewrite(e, issue_type)
407 raise e
408 else:
--> 409 raise e.with_traceback(None)
ConstantInferenceError: Failed in nopython mode pipeline (step: nopython rewrites)
Constant inference not possible for: $102build_string.16 + $100format_value.14
File "../../../../opt/anaconda3/envs/spatial/lib/python3.9/site-packages/pycisTopic/diff_features.py", line 1042:
def subset_array_second_axis(arr, col_indices):
<source elided>
if np.min(col_indices) < -arr.shape[1]:
raise IndexError(f"index {np.min(col_indices)} is out of bounds for axis 1 with size {arr.shape[1]}")
^
<Figure size 640x480 with 0 Axes>
Any idea why this might be happening? I tried updating Numba to the latest version but this then breaks the UMAP visualization.
Here is the detail of the environment I am currently using.
# packages in environment at /Users/josephineyates/opt/anaconda3/envs/spatial:
#
# Name Version Build Channel
adjusttext 0.8 pypi_0 pypi
aiohttp 3.8.4 pypi_0 pypi
aiohttp-cors 0.7.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
alabaster 0.7.13 pypi_0 pypi
anndata 0.8.0 pypi_0 pypi
annoy 1.17.3 pypi_0 pypi
ansiwrap 0.8.4 pypi_0 pypi
anyio 3.6.2 pypi_0 pypi
appnope 0.1.3 pypi_0 pypi
arboreto 0.1.6 pypi_0 pypi
argon2-cffi 21.3.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.2.3 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
astor 0.8.1 pypi_0 pypi
asttokens 2.2.1 pypi_0 pypi
async-timeout 4.0.2 pypi_0 pypi
attrs 22.2.0 pypi_0 pypi
autograd 1.6.2 pypi_0 pypi
autograd-gamma 0.5.0 pypi_0 pypi
babel 2.12.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
bbknn 1.6.0 pypi_0 pypi
beautifulsoup4 4.11.2 pypi_0 pypi
blas 1.0 mkl
bleach 6.0.0 pypi_0 pypi
blessed 1.20.0 pypi_0 pypi
blosc2 2.0.0 pypi_0 pypi
bokeh 3.2.0 pypi_0 pypi
boltons 23.0.0 pypi_0 pypi
brotlipy 0.7.0 py39h9ed2024_1003
bs4 0.0.1 pypi_0 pypi
bzip2 1.0.8 h1de35cc_0
ca-certificates 2023.01.10 hecd8cb5_0
cachetools 5.3.1 pypi_0 pypi
catheat 0.2.0 pypi_0 pypi
cattrs 23.1.2 pypi_0 pypi
certifi 2022.12.7 py39hecd8cb5_0
cffi 1.15.1 py39h6c40b1e_3
chardet 5.2.0 pypi_0 pypi
charset-normalizer 3.1.0 pypi_0 pypi
click 8.1.3 pypi_0 pypi
cloudpickle 2.2.1 pypi_0 pypi
colorful 0.5.5 pypi_0 pypi
comm 0.1.2 pypi_0 pypi
contourpy 1.0.7 pypi_0 pypi
cryptography 39.0.1 py39hf6deb26_0
ctxcore 0.2.0 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cykhash 2.0.1 pypi_0 pypi
cython 0.29.36 pypi_0 pypi
cytoolz 0.12.1 pypi_0 pypi
dask 2023.6.1 pypi_0 pypi
dask-image 2022.9.0 pypi_0 pypi
dataclasses-json 0.6.0 pypi_0 pypi
debugpy 1.6.6 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
decoupler 1.3.4 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
dill 0.3.6 pypi_0 pypi
distlib 0.3.7 pypi_0 pypi
distributed 2023.6.1 pypi_0 pypi
docrep 0.3.2 pypi_0 pypi
docutils 0.18.1 pypi_0 pypi
entrypoints 0.4 pypi_0 pypi
et-xmlfile 1.1.0 pypi_0 pypi
exceptiongroup 1.1.3 pypi_0 pypi
executing 1.2.0 pypi_0 pypi
fasteners 0.18 pypi_0 pypi
fastjsonschema 2.16.3 pypi_0 pypi
fbpca 1.0 pypi_0 pypi
ffmpeg 4.3 h0a44026_0 pytorch
filelock 3.9.0 py39hecd8cb5_0
flit-core 3.6.0 pyhd3eb1b0_0
fonttools 4.39.0 pypi_0 pypi
formulaic 0.6.4 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
freetype 2.12.1 hd8bbffd_0
frozendict 2.3.8 pypi_0 pypi
frozenlist 1.3.3 pypi_0 pypi
fsspec 2023.3.0 pypi_0 pypi
future 0.18.3 pypi_0 pypi
gensim 4.3.2 pypi_0 pypi
geoparse 2.0.3 pypi_0 pypi
geosketch 1.2 pypi_0 pypi
gettext 0.21.0 h7535e17_0
giflib 5.2.1 h6c40b1e_3
globre 0.1.5 pypi_0 pypi
gmp 6.2.1 he9d5cce_3
gmpy2 2.1.2 py39hd5de756_0
gnutls 3.6.15 hed9c0bf_0
google-api-core 2.11.1 pypi_0 pypi
google-auth 2.23.0 pypi_0 pypi
googleapis-common-protos 1.60.0 pypi_0 pypi
gpustat 1.1.1 pypi_0 pypi
grpcio 1.58.0 pypi_0 pypi
gseapy 1.0.4 pypi_0 pypi
gtfparse 2.0.1 pypi_0 pypi
h5py 3.8.0 pypi_0 pypi
harmonypy 0.0.9 pypi_0 pypi
hmmlearn 0.3.0 pypi_0 pypi
icu 58.2 h0a44026_3
idna 3.4 py39hecd8cb5_0
igraph 0.10.4 pypi_0 pypi
imagecodecs 2023.7.4 pypi_0 pypi
imageio 2.26.0 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 6.0.0 pypi_0 pypi
importlib-resources 5.12.0 pypi_0 pypi
infercnvpy 0.4.1 pypi_0 pypi
inflect 6.0.2 pypi_0 pypi
intel-openmp 2021.4.0 hecd8cb5_3538
interface-meta 1.3.0 pypi_0 pypi
interlap 0.2.7 pypi_0 pypi
intervaltree 3.1.0 pypi_0 pypi
ipykernel 6.21.3 pypi_0 pypi
ipympl 0.9.3 pypi_0 pypi
ipython 8.11.0 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
ipywidgets 8.0.4 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.18.2 pypi_0 pypi
jinja2 3.1.2 py39hecd8cb5_0
joblib 1.2.0 pypi_0 pypi
jpeg 9e h6c40b1e_1
jsonpointer 2.3 pypi_0 pypi
jsonschema 4.17.3 pypi_0 pypi
jupyter 1.0.0 pypi_0 pypi
jupyter-client 8.0.3 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-core 5.2.0 pypi_0 pypi
jupyter-events 0.6.3 pypi_0 pypi
jupyter-server 2.4.0 pypi_0 pypi
jupyter-server-terminals 0.4.4 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-widgets 3.0.5 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
lame 3.100 h1de35cc_0
lazy-loader 0.1 pypi_0 pypi
lcms2 2.12 hf1fd2bf_0
lda 2.0.0 pypi_0 pypi
leidenalg 0.9.1 pypi_0 pypi
lerc 3.0 he9d5cce_0
levenshtein 0.21.1 pypi_0 pypi
libcxx 14.0.6 h9765a3e_0
libdeflate 1.17 hb664fd8_0
libffi 3.4.2 hecd8cb5_6
libiconv 1.16 hca72f7f_2
libidn2 2.3.2 h9ed2024_0
libpng 1.6.39 h6c40b1e_0
libtasn1 4.16.0 h9ed2024_0
libtiff 4.5.0 hcec6c5f_2
libunistring 0.9.10 h9ed2024_0
libwebp 1.2.4 hf6ce154_1
libwebp-base 1.2.4 h6c40b1e_1
libxml2 2.9.14 hbf8cd5e_0
lifelines 0.27.7 pypi_0 pypi
llvm-openmp 14.0.6 h0dcd299_0
llvmlite 0.38.1 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loompy 3.0.7 pypi_0 pypi
loomxpy 0.4.2 pypi_0 pypi
louvain 0.8.0 pypi_0 pypi
lxml 4.9.2 pypi_0 pypi
lz4 4.3.2 pypi_0 pypi
lz4-c 1.9.4 hcec6c5f_0
maca-python 1.0.1 pypi_0 pypi
macs2 2.2.9.1 pypi_0 pypi
macs3 3.0.0b3 pypi_0 pypi
markupsafe 2.1.2 pypi_0 pypi
marshmallow 3.20.1 pypi_0 pypi
matplotlib 3.7.1 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
matplotlib-scalebar 0.8.1 pypi_0 pypi
mistune 2.0.5 pypi_0 pypi
mkl 2021.4.0 hecd8cb5_637
mkl-service 2.4.0 py39h9ed2024_0
mkl_fft 1.3.1 py39h4ab4a9b_0
mkl_random 1.2.2 py39hb2f4e1b_0
mpc 1.1.0 h6ef4df4_1
mpfr 4.0.2 h9066e36_1
mpmath 1.2.1 py39hecd8cb5_0
msgpack 1.0.5 pypi_0 pypi
multidict 6.0.4 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
mypy-extensions 1.0.0 pypi_0 pypi
natsort 8.3.1 pypi_0 pypi
nbclassic 0.5.3 pypi_0 pypi
nbclient 0.7.2 pypi_0 pypi
nbconvert 7.2.10 pypi_0 pypi
nbformat 5.7.3 pypi_0 pypi
nbsphinx 0.9.3 pypi_0 pypi
nbsphinx-link 1.3.0 pypi_0 pypi
ncls 0.0.68 pypi_0 pypi
ncurses 6.4 hcec6c5f_0
nest-asyncio 1.5.6 pypi_0 pypi
nettle 3.7.3 h230ac6f_1
networkx 3.0 pypi_0 pypi
notebook 6.5.3 pypi_0 pypi
notebook-shim 0.2.2 pypi_0 pypi
numba 0.55.2 pypi_0 pypi
numcodecs 0.11.0 pypi_0 pypi
numexpr 2.8.4 pypi_0 pypi
numpy 1.22.4 pypi_0 pypi
numpy-groupies 0.9.22 pypi_0 pypi
numpydoc 1.5.0 pypi_0 pypi
nvidia-ml-py 12.535.108 pypi_0 pypi
omnipath 1.0.6 pypi_0 pypi
opencensus 0.11.3 pypi_0 pypi
opencensus-context 0.1.3 pypi_0 pypi
opencv-python 4.7.0.72 pypi_0 pypi
openh264 2.1.1 h8346a28_0
openpyxl 3.1.2 pypi_0 pypi
openssl 1.1.1t hca72f7f_0
packaging 23.0 pypi_0 pypi
pandas 1.5.0 pypi_0 pypi
pandocfilters 1.5.0 pypi_0 pypi
papermill 2.4.0 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
partd 1.3.0 pypi_0 pypi
patsy 0.5.3 pypi_0 pypi
pbr 3.1.1 pypi_0 pypi
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.4.0 pypi_0 pypi
pims 0.6.1 pypi_0 pypi
pip 23.2.1 pypi_0 pypi
platformdirs 3.1.1 pypi_0 pypi
polars 0.19.3 pypi_0 pypi
prometheus-client 0.16.0 pypi_0 pypi
prompt-toolkit 3.0.38 pypi_0 pypi
protobuf 4.24.3 pypi_0 pypi
psutil 5.9.4 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
py-cpuinfo 9.0.0 pypi_0 pypi
py-spy 0.3.14 pypi_0 pypi
pyarrow 12.0.1 pypi_0 pypi
pyasn1 0.5.0 pypi_0 pypi
pyasn1-modules 0.3.0 pypi_0 pypi
pybedtools 0.9.1 pypi_0 pypi
pybigwig 0.3.22 pypi_0 pypi
pybiomart 0.2.0 pypi_0 pypi
pycistopic 1.0.3.dev18+ge563fb6 pypi_0 pypi
pycparser 2.21 pyhd3eb1b0_0
pydantic 1.10.6 pypi_0 pypi
pyfasta 0.5.2 pypi_0 pypi
pygments 2.14.0 pypi_0 pypi
pynndescent 0.5.8 pypi_0 pypi
pyometiff 0.0.13 pypi_0 pypi
pyopenssl 23.0.0 py39hecd8cb5_0
pyparsing 3.0.9 pypi_0 pypi
pyranges 0.0.127 pypi_0 pypi
pyreadr 0.4.7 pypi_0 pypi
pyrsistent 0.19.3 pypi_0 pypi
pysam 0.21.0 pypi_0 pypi
pyscenic 0.12.1+6.g31d51a1 pypi_0 pypi
pysocks 1.7.1 py39hecd8cb5_0
python 3.9.16 h218abb5_2
python-dateutil 2.8.2 pypi_0 pypi
python-igraph 0.10.4 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
python-levenshtein 0.21.1 pypi_0 pypi
pytoml 0.1.21 pypi_0 pypi
pytz 2022.7.1 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 25.0.1 pypi_0 pypi
qtconsole 5.4.1 pypi_0 pypi
qtpy 2.3.0 pypi_0 pypi
rapidfuzz 3.3.0 pypi_0 pypi
ray 2.7.0 pypi_0 pypi
readline 8.2 hca72f7f_0
requests 2.28.2 pypi_0 pypi
requests-cache 1.1.0 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rsa 4.9 pypi_0 pypi
scanorama 1.7.3 pypi_0 pypi
scanpy 1.9.3 pypi_0 pypi
scikit-image 0.20.0 pypi_0 pypi
scikit-learn 1.2.2 pypi_0 pypi
scipy 1.9.1 pypi_0 pypi
scrublet 0.2.3 pypi_0 pypi
seaborn 0.11.2 pypi_0 pypi
send2trash 1.8.0 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 68.0.0 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_1
sklearn 0.0.post1 pypi_0 pypi
slicerator 1.1.0 pypi_0 pypi
smart-open 6.4.0 pypi_0 pypi
sniffio 1.3.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sorted-nearest 0.0.39 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.4 pypi_0 pypi
spagcn 1.2.5 pypi_0 pypi
sphinx 7.2.6 pypi_0 pypi
sphinx-rtd-theme 1.3.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.7 pypi_0 pypi
sphinxcontrib-devhelp 1.0.5 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.4 pypi_0 pypi
sphinxcontrib-jquery 4.1 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.6 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.9 pypi_0 pypi
sqlite 3.41.1 h6c40b1e_0
squidpy 1.2.3 pypi_0 pypi
stack-data 0.6.2 pypi_0 pypi
statannot 0.2.3 pypi_0 pypi
statannotations 0.5.0 pypi_0 pypi
statsmodels 0.13.5 pypi_0 pypi
stdlib-list 0.8.0 pypi_0 pypi
sympy 1.11.1 py39hecd8cb5_0
tables 3.8.0 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tblib 2.0.0 pypi_0 pypi
tenacity 8.2.3 pypi_0 pypi
terminado 0.17.1 pypi_0 pypi
texttable 1.6.7 pypi_0 pypi
textwrap3 0.9.2 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2023.2.28 pypi_0 pypi
tinycss2 1.2.1 pypi_0 pypi
tk 8.6.12 h5d9f67b_0
tmtoolkit 0.11.2 pypi_0 pypi
toolz 0.12.0 pypi_0 pypi
torch 1.10.2 pypi_0 pypi
torchaudio 2.0.0 py39_cpu pytorch
torchvision 0.11.3 pypi_0 pypi
tornado 6.2 pypi_0 pypi
tqdm 4.65.0 pypi_0 pypi
traitlets 5.9.0 pypi_0 pypi
tspex 0.6.3 pypi_0 pypi
typing 3.7.4.3 pypi_0 pypi
typing-extensions 4.5.0 pypi_0 pypi
typing-inspect 0.9.0 pypi_0 pypi
typing_extensions 4.4.0 py39hecd8cb5_0
tzdata 2022g h04d1e81_0
umap-learn 0.5.3 pypi_0 pypi
uri-template 1.2.0 pypi_0 pypi
url-normalize 1.4.3 pypi_0 pypi
urllib3 1.26.15 pypi_0 pypi
validators 0.20.0 pypi_0 pypi
virtualenv 20.21.0 pypi_0 pypi
wcwidth 0.2.6 pypi_0 pypi
webcolors 1.12 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.5.1 pypi_0 pypi
wget 3.2 pypi_0 pypi
wheel 0.38.4 py39hecd8cb5_0
widgetsnbextension 4.0.5 pypi_0 pypi
wrapt 1.15.0 pypi_0 pypi
xarray 2023.2.0 pypi_0 pypi
xlrd 2.0.1 pypi_0 pypi
xyzservices 2023.5.0 pypi_0 pypi
xz 5.2.10 h6c40b1e_1
yarl 1.8.2 pypi_0 pypi
zarr 2.14.2 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.15.0 pypi_0 pypi
zlib 1.2.13 h4dc903c_0
zstd 1.5.2 hcb37349_0
Thank you for your help!
Hi again,
Just to give some more information, I can run find_diff_features without any errors by directly copying the source code and removing the numba decorators.
Hi Ghuls, Thank you for answering! So installing numba >=0.57.0 unfortunately breaks the UMAP implementation. I was running this on a Mac M1 and maybe this is related - I know there have been issues previously running UMAP on M1 chips. In any case, I've switched to running on the cluster where a fresh install of everything with latest versions worked. Leaving this here in case someone else runs into this issue. Thank you again for your time!
@josephineyates Does updating pynndescent help? https://github.com/aertslab/pycisTopic/issues/92#issuecomment-1735438244
Hello @ghuls @SeppeDeWinter
I got the same following error by running:
from pycisTopic.diff_features import * imputed_acc_obj = impute_accessibility(cistopic_obj, selected_cells=None, selected_regions=None, scale_factor=106) normalized_imputed_acc_obj = normalize_scores(imputed_acc_obj, scale_factor=104) variable_regions = find_highly_variable_features(normalized_imputed_acc_obj, plot = False) markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='celltype', var_features=variable_regions, split_pattern = '-')
Here is the error:
ConstantInferenceError Traceback (most recent call last) /Users/stur/Teaseq/Scenicplus/PB2/Scenicplus_PB2.ipynb Cell 67 line 1 ----> 1 markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='celltype', var_features=variable_regions, split_pattern = '-')
File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pycisTopic/diff_features.py:800, in find_diff_features(cistopic_obj, imputed_features_obj, variable, var_features, contrasts, adjpval_thr, log2fc_thr, split_pattern, n_cpu, **kwargs) 798 ray.shutdown() 799 else: --> 800 markers_list = [ 801 markers( 802 subset_imputed_features_obj, 803 barcode_groups[i], 804 contrasts_names[i], 805 adjpval_thr=adjpval_thr, 806 log2fc_thr=log2fc_thr, 807 n_cpu=1, 808 ) 809 for i in range(len(contrasts)) 810 ] 812 markers_dict = { 813 contrasts_name: marker 814 for contrasts_name, marker in zip(contrasts_names, markers_list) 815 } 817 return markers_dict
File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pycisTopic/diff_features.py:801, in
File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pycisTopic/diff_features.py:884, in markers(input_mat, barcode_group, contrast_name, adjpval_thr, log2fc_thr, n_cpu) 882 bg_mat = mat[:, bg_cells_index].toarray() 883 else: --> 884 fg_mat = subset_array_second_axis(arr=mat, col_indices=fg_cells_index) 885 bg_mat = subset_array_second_axis(arr=mat, col_indices=bg_cells_index) 887 log.info(f"Computing p-value for {contrast_name}")
File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/numba/core/dispatcher.py:480, in _DispatcherBase._compile_for_args(self, *args, **kws) 476 error_rewrite(e, 'interpreter') 477 except errors.ConstantInferenceError as e: 478 # this is from trying to infer something as constant when it isn't 479 # or isn't supported as a constant --> 480 error_rewrite(e, 'constant_inference') 481 except Exception as e: 482 if config.SHOW_HELP:
File /opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/numba/core/dispatcher.py:409, in _DispatcherBase._compile_for_args.
ConstantInferenceError: Failed in nopython mode pipeline (step: nopython rewrites) Constant inference not possible for: $102build_string.16 + $100format_value.14
File "../../../../opt/homebrew/Caskroom/miniconda/base/lib/python3.10/site-packages/pycisTopic/diff_features.py", line 1042:
def subset_array_second_axis(arr, col_indices):
Can you help me to troubleshoot this?
Best,
Steven
