[BUG]

[wuxiangning]

MY code:
import subprocess

构建 PySCENIC 命令

command = [
r"E:\Ana\envs\pyscenic\Scripts\pyscenic.exe", "ctx", "step1out_grn1.tsv",
"hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather",
"hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather",
"--annotations_fname", "motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl",
"--expression_mtx_fname", "LIHC_9Neu_random300_cells.loom",
"--mode", "dask_multiprocessing",
"--output", "step2out_ctx——tes.tsv",
"--num_workers", "14"
]

运行命令并捕获输出和错误

result = subprocess.run(command, capture_output=True, text=True)

打印标准输出和错误信息

print("stdout:", result.stdout)
print("stderr:", result.stderr)

the error messeage:
stdout:
stderr:
2025-02-25 22:10:17,997 - pyscenic.cli.pyscenic - INFO - Creating modules.

2025-02-25 22:10:18,163 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2025-02-25 22:10:18,263 - pyscenic.utils - INFO - Calculating Pearson correlations.

2025-02-25 22:10:18,323 - pyscenic.utils - WARNING - Note on correlation calculation: the default behaviour for calculating the correlations has changed after pySCENIC verion 0.9.16. Previously, the default was to calculate the correlation between a TF and target gene using only cells with non-zero expression values (mask_dropouts=True). The current default is now to use all cells to match the behavior of the R verision of SCENIC. The original settings can be retained by setting 'rho_mask_dropouts=True' in the modules_from_adjacencies function, or '--mask_dropouts' from the CLI.
Dropout masking is currently set to [False].

2025-02-25 22:10:22,401 - pyscenic.utils - INFO - Creating modules.

2025-02-25 22:10:39,796 - pyscenic.cli.pyscenic - INFO - Loading databases.

2025-02-25 22:10:39,931 - pyscenic.cli.pyscenic - INFO - Calculating regulons.
Traceback (most recent call last):
File "E:\Ana\envs\pyscenic\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "E:\Ana\envs\pyscenic\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "E:\Ana\envs\pyscenic\Scripts\pyscenic.exe_main.py", line 7, in
File "E:\Ana\envs\pyscenic\lib\site-packages\pyscenic\cli\pyscenic.py", line 713, in main
args.func(args)
File "E:\Ana\envs\pyscenic\lib\site-packages\pyscenic\cli\pyscenic.py", line 236, in prune_targets_command
df_motifs = calc_func(
File "E:\Ana\envs\pyscenic\lib\site-packages\pyscenic\prune.py", line 424, in prune2df
return _distributed_calc(
File "E:\Ana\envs\pyscenic\lib\site-packages\pyscenic\prune.py", line 351, in _distributed_calc
return create_graph().compute(
File "E:\Ana\envs\pyscenic\lib\site-packages\pyscenic\prune.py", line 340, in create_graph
return aggregate_func(
File "E:\Ana\envs\pyscenic\lib\site-packages\dask_expr\io_delayed.py", line 114, in from_delayed
if len(dfs) == 0:
TypeError: object of type 'generator' has no len()

thanks！