pySCENIC
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Published
20 hours ago •
aertslab
aertslab
[BUG] grnboost2 TypeError: Must supply at least one delayed object
Describe the bug
Running GRNBoost2 produces an error at the very last step. Reproducible with the tutorial (https://pyscenic.readthedocs.io/en/latest/tutorial.html) using the GSE60361_C1-3005-Expression.txt dataset.
Installing arboreto from source did not help
Steps to reproduce the behavior
- Command run when the error occurred:
import os
import glob
import pickle
import pandas as pd
import numpy as np
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
import seaborn as sns
DATA_FOLDER="/home/ali/Dokumente/15d _Organoids_Multiome/Separate/SCENIC/CommittedMesoderm"
RESOURCES_FOLDER="/home/ali/Dokumente/15d _Organoids_Multiome/Separate/SCENIC/pySCENIC"
MATRIX_FOLDER="/home/ali/Dokumente/15d _Organoids_Multiome/Separate/SCENIC/pySCENIC/Matrix"
SCHEDULER="123.122.8.24:8786"
DATABASES_GLOB = os.path.join(RESOURCES_FOLDER, "hg38_*.genes_vs_motifs.rankings.feather")
MOTIF_ANNOTATIONS_FNAME = os.path.join(RESOURCES_FOLDER, "motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl")
MM_TFS_FNAME = '/home/ali/pySCENIC/resources/hs_hgnc_tfs.txt'
SC_EXP_FNAME = os.path.join(MATRIX_FOLDER, "Cardiac-Cimmitted Cells_matrix.csv")
REGULONS_FNAME = os.path.join(DATA_FOLDER, "regulons.p")
MOTIFS_FNAME = os.path.join(DATA_FOLDER, "motifs.csv")
ex_matrix = pd.read_csv(SC_EXP_FNAME, sep=',', header=0, index_col=0).T
tf_names = 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]
adjacencies = grnboost2(ex_matrix, tf_names=tf_names, verbose=True)
...
- Error encountered:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[17], line 2
1 #single cell expression profiles are used to infer co-expression modules
----> 2 adjacencies = grnboost2(ex_matrix, tf_names=tf_names, verbose=True)
File ~/anaconda3/envs/pySCENIC/lib/python3.12/site-packages/arboreto/algo.py:39, in grnboost2(expression_data, gene_names, tf_names, client_or_address, early_stop_window_length, limit, seed, verbose)
10 def grnboost2(expression_data,
11 gene_names=None,
12 tf_names='all',
(...)
16 seed=None,
17 verbose=False):
18 """
19 Launch arboreto with [GRNBoost2] profile.
20
(...)
36 :return: a pandas DataFrame['TF', 'target', 'importance'] representing the inferred gene regulatory links.
37 """
---> 39 return diy(expression_data=expression_data, regressor_type='GBM', regressor_kwargs=SGBM_KWARGS,
40 gene_names=gene_names, tf_names=tf_names, client_or_address=client_or_address,
41 early_stop_window_length=early_stop_window_length, limit=limit, seed=seed, verbose=verbose)
File ~/anaconda3/envs/pySCENIC/lib/python3.12/site-packages/arboreto/algo.py:120, in diy(expression_data, regressor_type, regressor_kwargs, gene_names, tf_names, client_or_address, early_stop_window_length, limit, seed, verbose)
117 if verbose:
118 print('creating dask graph')
--> 120 graph = create_graph(expression_matrix,
121 gene_names,
122 tf_names,
123 client=client,
124 regressor_type=regressor_type,
125 regressor_kwargs=regressor_kwargs,
126 early_stop_window_length=early_stop_window_length,
127 limit=limit,
128 seed=seed)
130 if verbose:
131 print('{} partitions'.format(graph.npartitions))
File ~/anaconda3/envs/pySCENIC/lib/python3.12/site-packages/arboreto/core.py:450, in create_graph(expression_matrix, gene_names, tf_names, regressor_type, regressor_kwargs, client, target_genes, limit, include_meta, early_stop_window_length, repartition_multiplier, seed)
448 # gather the DataFrames into one distributed DataFrame
449 all_links_df = from_delayed(delayed_link_dfs, meta=_GRN_SCHEMA)
--> 450 all_meta_df = from_delayed(delayed_meta_dfs, meta=_META_SCHEMA)
452 # optionally limit the number of resulting regulatory links, descending by top importance
453 if limit:
File ~/anaconda3/envs/pySCENIC/lib/python3.12/site-packages/dask_expr/io/_delayed.py:115, in from_delayed(dfs, meta, divisions, prefix, verify_meta)
112 dfs = [dfs]
114 if len(dfs) == 0:
--> 115 raise TypeError("Must supply at least one delayed object")
117 if meta is None:
118 meta = delayed(make_meta)(dfs[0]).compute()
TypeError: Must supply at least one delayed object
- pySCENIC version: [0.12.1+8.gd2309fe]
- Installation method: [pip]
- Run environment: [Jupyter notebook]
- OS: [e.g. Ubuntu]
- Package versions: [obtain using
pip freeze,conda list, or skip this if using Docker/Singularity]:
# packages in environment at /home/ali/anaconda3/envs/pySCENIC:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiohttp 3.9.5 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
anyio 4.4.0 pypi_0 pypi
arboreto 0.1.6 pyh3252c3a_0 bioconda
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
aws-c-auth 0.7.22 hbd3ac97_10 conda-forge
aws-c-cal 0.7.1 h87b94db_1 conda-forge
aws-c-common 0.9.23 h4ab18f5_0 conda-forge
aws-c-compression 0.2.18 he027950_7 conda-forge
aws-c-event-stream 0.4.2 h7671281_15 conda-forge
aws-c-http 0.8.2 he17ee6b_6 conda-forge
aws-c-io 0.14.10 h826b7d6_1 conda-forge
aws-c-mqtt 0.10.4 hcd6a914_8 conda-forge
aws-c-s3 0.6.0 h365ddd8_2 conda-forge
aws-c-sdkutils 0.1.16 he027950_3 conda-forge
aws-checksums 0.1.18 he027950_7 conda-forge
aws-crt-cpp 0.27.3 hda66527_2 conda-forge
aws-sdk-cpp 1.11.329 h46c3b66_9 conda-forge
azure-core-cpp 1.12.0 h830ed8b_0 conda-forge
azure-identity-cpp 1.8.0 hdb0d106_1 conda-forge
azure-storage-blobs-cpp 12.11.0 ha67cba7_1 conda-forge
azure-storage-common-cpp 12.6.0 he3f277c_1 conda-forge
azure-storage-files-datalake-cpp 12.10.0 h29b5301_1 conda-forge
babel 2.15.0 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
bokeh 3.5.0 pyhd8ed1ab_0 conda-forge
boltons 24.0.0 pypi_0 pypi
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py312h30efb56_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.2 h4bc722e_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py312hf06ca03_0 conda-forge
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pypi_0 pypi
contourpy 1.2.1 py312h8572e83_0 conda-forge
ctxcore 0.2.0 pypi_0 pypi
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.3 py312h98912ed_0 conda-forge
dask 2024.7.0 pyhd8ed1ab_0 conda-forge
dask-core 2024.7.0 pyhd8ed1ab_0 conda-forge
dask-expr 1.1.8 pypi_0 pypi
dask-glm 0.3.2 pypi_0 pypi
dask-ml 2024.4.4 pypi_0 pypi
debugpy 1.8.2 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
dill 0.3.8 pypi_0 pypi
distributed 2024.7.0 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pypi_0 pypi
fastjsonschema 2.20.0 pypi_0 pypi
fonttools 4.53.1 py312h41a817b_0 conda-forge
fqdn 1.5.1 pypi_0 pypi
freetype 2.12.1 h267a509_2 conda-forge
frozendict 2.4.4 pypi_0 pypi
frozenlist 1.4.1 pypi_0 pypi
fsspec 2024.6.1 pyhff2d567_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
h11 0.14.0 pypi_0 pypi
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 pypi_0 pypi
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.5 pypi_0 pypi
httpx 0.27.0 pypi_0 pypi
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.7 pypi_0 pypi
importlib-metadata 8.0.0 pyha770c72_0 conda-forge
importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge
interlap 0.2.7 pypi_0 pypi
ipykernel 6.29.5 pypi_0 pypi
ipython 8.26.0 pypi_0 pypi
ipywidgets 8.1.3 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pypi_0 pypi
jsonpointer 3.0.0 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter 1.0.0 pypi_0 pypi
jupyter-client 8.6.2 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.2 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.2.4 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.11 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py312h8572e83_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libarrow 16.1.0 h34456a7_14_cpu conda-forge
libarrow-acero 16.1.0 he02047a_14_cpu conda-forge
libarrow-dataset 16.1.0 he02047a_14_cpu conda-forge
libarrow-substrait 16.1.0 hc9a23c6_14_cpu conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libgomp 14.1.0 h77fa898_0 conda-forge
libgoogle-cloud 2.26.0 h26d7fe4_0 conda-forge
libgoogle-cloud-storage 2.26.0 ha262f82_0 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libparquet 16.1.0 h9e5060d_14_cpu conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libthrift 0.19.0 hb90f79a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.16 hd590300_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loompy 3.0.7 pypi_0 pypi
lz4 4.3.3 py312h03f37cb_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 2.1.5 py312h98912ed_0 conda-forge
matplotlib-base 3.9.1 py312h9201f00_0 conda-forge
matplotlib-inline 0.1.7 pypi_0 pypi
mistune 3.0.2 pypi_0 pypi
msgpack-python 1.0.8 py312h2492b07_0 conda-forge
multidict 6.0.5 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
munkres 1.0.7 py_1 bioconda
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.4 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.3 pypi_0 pypi
notebook 7.2.1 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numexpr 2.10.1 pypi_0 pypi
numpy 2.0.0 py312h22e1c76_0 conda-forge
numpy-groupies 0.11.1 pypi_0 pypi
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4bc722e_2 conda-forge
orc 2.0.1 h17fec99_1 conda-forge
overrides 7.7.0 pypi_0 pypi
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py312h1d6d2e6_1 conda-forge
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pypi_0 pypi
pillow 10.4.0 py312h287a98d_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.2 pypi_0 pypi
prometheus-client 0.20.0 pypi_0 pypi
prompt-toolkit 3.0.47 pypi_0 pypi
psutil 6.0.0 py312h9a8786e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pypi_0 pypi
pynndescent 0.5.13 pypi_0 pypi
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyscenic 0.12.1+8.gd2309fe pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.4 h194c7f8_0_cpython conda-forge
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 2.0.7 pypi_0 pypi
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py312h98912ed_1 conda-forge
pyzmq 26.0.3 pypi_0 pypi
qhull 2020.2 h434a139_5 conda-forge
qtconsole 5.5.2 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rpds-py 0.19.0 pypi_0 pypi
s2n 1.4.17 he19d79f_0 conda-forge
scikit-learn 1.5.1 py312h775a589_0 conda-forge
scipy 1.14.0 py312hc2bc53b_1 conda-forge
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
send2trash 1.8.3 pypi_0 pypi
setuptools 71.0.3 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sniffio 1.3.1 pypi_0 pypi
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pypi_0 pypi
sparse 0.15.4 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.2 py312h085067d_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pypi_0 pypi
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tinycss2 1.3.0 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h9a8786e_0 conda-forge
tqdm 4.66.4 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
types-python-dateutil 2.9.0.20240316 pypi_0 pypi
tzdata 2024a h0c530f3_0 conda-forge
umap-learn 0.5.6 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.13 pypi_0 pypi
webcolors 24.6.0 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.11 pypi_0 pypi
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xyzservices 2024.6.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 pypi_0 pypi
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.19.2 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py312h3483029_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
...
