error in running "preprocess_sample.py"

[zincuum]

hello,
I ran the code python ./scripts/preprocess_sample.py directly from within preprocess_samples.sh, and encountered the following error. The expected reason is that there are differences in the number of rows among the files provided to the --readdepth option.

python3 /data/project/ccRCC/2025_ccRCC/DNA/0.Tools/ECOLE/scripts/preprocess_sample.py --readdepth /data/project/ccRCC/2025_ccRCC/DNA/3.Analysis/CNV/ECOLE/temp/ --output /data/project/ccRCC/2025_ccRCC/DNA/3.Analysis/CNV/ECOLE --target /data/project/ccRCC/2025_ccRCC/DNA/0.resource/T2T/bed/S31285117_selected_Covered.T2T_UCSC.bed
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 23/23 [00:15<00:00, 1.48it/s]
Traceback (most recent call last):
File "/data/project/ccRCC/2025_ccRCC/DNA/0.Tools/ECOLE/scripts/preprocess_sample.py", line 101, in
labeled_data = np.asarray(labeled_data)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (6955, 5) + inhomogeneous part.

[EshrakaAli]

I think you have to modify the python script to deal with it