ex.export_coverage fails with some probloms

[RaFenglei]

Hey Kai,

Running into an error when using the export_coverage function with mostly defaults:

2025-05-23 19:17:15 - INFO - Exporting fragments...
Processing cluster: 4
2025-05-23 19:17:18 - INFO - Computing coverage...

RuntimeError Traceback (most recent call last)
Cell In[252], line 13
10 subset = data[cluster_cells]
12 # 导出当前cluster的bw文件
---> 13 snap.ex.export_coverage(
14 adata=subset,
15 groupby="cluster", # 实际上这里只有当前cluster
16 out_dir=output_dir,
17 prefix=f"cluster_{cluster}_", # 文件名包含cluster名
18 suffix=".bw",
19 n_jobs=1, # 单线程更稳妥
20 normalization="RPKM"
21 )

File ~/miniconda3/envs/omicverse/lib/python3.9/site-packages/snapatac2/export/init.py:232, in export_coverage(adata, groupby, selections, bin_size, blacklist, normalization, include_for_norm, exclude_for_norm, min_frag_length, max_frag_length, counting_strategy, smooth_base, out_dir, prefix, suffix, output_format, compression, compression_level, tempdir, n_jobs)
229 compression = inferred_compression
231 n_jobs = None if n_jobs <= 0 else n_jobs
--> 232 return internal.export_coverage(
233 adata, list(groupby), bin_size, out_dir, prefix, suffix, output_format, counting_strategy,
234 selections, blacklist, normalization, include_for_norm, exclude_for_norm, min_frag_length,
235 max_frag_length, smooth_base, compression, compression_level, tempdir, n_jobs,
236 )

RuntimeError: Too many open files (os error 24)

Caused by:
Too many open files (os error 24)