pySCENIC [BUG] TypeError: Must supply at least one delayed object

TypeError: Must supply at least one delayed object

Input matrix

ex_matrix = pd.read_csv(SC_EXP_FNAME, sep='\t', header=0, index_col=0).T ex_matrix.head() GENE Mrpl15 Lypla1 Gm37988 Tcea1 Atp6v1h Rb1cc1 4732440D04Rik Pcmtd1 Gm26901 Rrs1 Adhfe1 Mybl1
BM_AAACCCAAGTCTAGAA.1 0.000000 1.098612 0.0 0.000000 0.000000 0.693147 0.000000 0.693147 0.0 0.693147 0.0 0.0

Code 1. Command run when the error occurred: import os import glob import pickle import pyscenic import pandas as pd import numpy as np import seaborn as sns import dask.dataframe as dd

from dask.diagnostics import ProgressBar

from arboreto.utils import load_tf_names from arboreto.algo import grnboost2

from ctxcore.rnkdb import FeatherRankingDatabase as RankingDatabase from pyscenic.utils import modules_from_adjacencies, load_motifs from pyscenic.prune import prune2df, df2regulons from pyscenic.aucell import aucell

DATA_FOLDER="C:/Users/S236282/Desktop/Itaconate data/pySCENIC" RESOURCES_FOLDER="C:/Users/S236282/Desktop/Itaconate data/pySCENIC" DATABASE_FOLDER = "C:/Users/S236282/Desktop/Itaconate data/pySCENIC"

DATABASES_GLOB = os.path.join(DATA_FOLDER, "mm10_*.genes_vs_motifs.rankings.feather") MOTIF_ANNOTATIONS_FNAME = os.path.join(RESOURCES_FOLDER, "motifs-v10nr_clustnr_mgi.tbl")

MM_TFS_FNAME = os.path.join(RESOURCES_FOLDER, 'allTFs_mm.txt') SC_EXP_FNAME = os.path.join(RESOURCES_FOLDER, "Expression_data.txt")

ADJACENCIES_FNAME = os.path.join(RESOURCES_FOLDER, "adjacencies.tsv") MODULES_FNAME = os.path.join(RESOURCES_FOLDER, "modules.p") MOTIFS_FNAME = os.path.join(RESOURCES_FOLDER, "motifs.csv") REGULONS_FNAME = os.path.join(RESOURCES_FOLDER, "regulons.p")

N_SAMPLES = 500

ex_matrix = pd.read_csv(SC_EXP_FNAME, sep='\t', header=0, index_col=0).T ex_matrix.head() ex_matrix.shape

tf_name = load_tf_names(MM_TFS_FNAME)

db_fnames = glob.glob(DATABASES_GLOB)

def name(fname): return os.path.splitext(os.path.basename(fname))[0]

dbs = [RankingDatabase(fname=fname, name=name(fname)) for fname in db_fnames] dbs

filtered_tf_name = list(intersection)

adjacencies = grnboost2(expression_data=ex_matrix, tf_names= tf_name, verbose=True) adjancencies.head()

2. Error encountered:

adjacencies = grnboost2(expression_data=ex_matrix, tf_names= tf_name, verbose=True) preparing dask client parsing input creating dask graph shutting down client and local cluster finished Traceback (most recent call last): File "", line 1, in File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\algo.py", line 39, in grnboost2 return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\algo.py", line 120, in diy graph = create_graph(expression_matrix, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\arboreto\core.py", line 450, in create_graph all_meta_df = from_delayed(delayed_meta_dfs, meta=_META_SCHEMA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\S236282\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\LocalCache\local-packages\Python311\site-packages\dask_expr\io_delayed.py", line 115, in from_delayed raise TypeError("Must supply at least one delayed object") TypeError: Must supply at least one delayed object

Expected behavior A clear and concise description of what you expected to happen.

Please complete the following information:

pySCENIC version: 0.12.1
Installation method: Pip
Run environment: Python 3.11.9
OS: Windows
Package versions:
aiohappyeyeballs==2.4.3 aiohttp==3.10.10 aiosignal==1.3.1 arboreto==0.1.6 attrs==24.2.0 bokeh==3.6.0 boltons==24.0.0 certifi==2024.8.30 charset-normalizer==3.4.0 click==8.1.7 cloudpickle==3.1.0 colorama==0.4.6 contourpy==1.3.0 ctxcore==0.2.0 cycler==0.12.1 cytoolz==1.0.0 dask==2024.10.0 dask-expr==1.1.16 dill==0.3.9 distributed==2024.2.1 fonttools==4.54.1 frozendict==2.4.6 frozenlist==1.5.0 fsspec==2024.10.0 h5py==3.12.1 idna==3.10 importlib_metadata==8.5.0 interlap==0.2.7 Jinja2==3.1.4 joblib==1.4.2 kiwisolver==1.4.7 llvmlite==0.43.0 locket==1.0.0 loompy==3.0.7 lz4==4.3.3 MarkupSafe==3.0.2 matplotlib==3.9.2 msgpack==1.1.0 multidict==6.1.0 multiprocessing_on_dill==3.5.0a4 networkx==3.4.2 numba==0.60.0 numexpr==2.10.1 numpy==2.0.2 numpy-groupies==0.11.2 packaging==24.1 pandas==2.2.3 partd==1.4.2 pillow==11.0.0 propcache==0.2.0 psutil==6.1.0 pyarrow==18.0.0 pynndescent==0.5.13 pyparsing==3.2.0 pyscenic==0.12.1 python-dateutil==2.9.0.post0 pytz==2024.2 PyYAML==6.0.2 requests==2.32.3 scikit-learn==1.5.2 scipy==1.14.1 seaborn==0.13.2 six==1.16.0 sortedcontainers==2.4.0 tblib==3.0.0 threadpoolctl==3.5.0 toolz==1.0.0 tornado==6.4.1 tqdm==4.66.6 tzdata==2024.2 umap-learn==0.5.7 urllib3==2.2.3 xyzservices==2024.9.0 yarl==1.17.1 zict==3.0.0 zipp==3.20.2

Nov 05 '24 18:11 Achiraa

Hi, It looks like issue #561. It might be linked to your dask-expr version (1.1.16) ? Best

Nov 13 '24 16:11 meriadecmorrier

Thank you. Unfortunately, it didn't work for me. it raised another error.

TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object

Nov 15 '24 14:11 Achiraa

I'm having the same bug, did you find a solution?

Nov 23 '24 22:11 olaf-c

Hi, I was not able to resolve this issue, but I tried using docker approach. It works and is easy. Here is the link: https://pyscenic.readthedocs.io/en/latest/installation.html

Nov 25 '24 15:11 Achiraa

This issue is caused by the create_graph function in arboreto.core. To resolve it, simply comment out the second command. While this error has already been fixed on GitHub, it has not yet been addressed in version 0.1.6 of the package.

Jan 02 '25 12:01 ruoyeruolan

The original problem posted here ([TypeError: Must supply at least one delayed object) should be fixed if you install via bioconda, as I just pinned the respective dask-expr<1.0.0 version in the arboreto package. So this should now install a working version of pyscenic:

conda create -n pyscenic -c conda-forge -b bioconda pyscenic

The original suggestion for this pinning comes from a comment in one of the issues here.

Nov 18 '25 13:11 dlaehnemann