snap.tl.macs3 error

Hello!

I am trying to follow your tutorial [https://kzhang.org/SnapATAC2/version/2.6/tutorials/diff.html] to analyze my dataset. But I got error "RuntimeError: Some worker process has died unexpectedly" (error message below) when I am running snap.tl.macs3(adata, groupby='leiden', n_jobs=1). Could you please help?

2024-09-05 16:39:33 - INFO - Exporting fragments...
2024-09-05 16:39:50 - INFO - Calling peaks...
  0%|          | 0/8 [00:00<?, ?it/s]Process SpawnPoolWorker-25:
Traceback (most recent call last):
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/multiprocess/process.py", line 314, in _bootstrap
    self.run()
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/multiprocess/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/multiprocess/pool.py", line 114, in worker
    task = get()
           ^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/multiprocess/queues.py", line 387, in get
    return _ForkingPickler.loads(res)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/dill/_dill.py", line 303, in loads
    return load(file, ignore, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/dill/_dill.py", line 289, in load
    return Unpickler(file, ignore=ignore, **kwds).load()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/dill/_dill.py", line 444, in load
    obj = StockUnpickler.load(self)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/dill/_dill.py", line 434, in find_class
    return StockUnpickler.find_class(self, module, name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/__init__.py", line 2, in <module>
    from . import preprocessing as pp
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/preprocessing/__init__.py", line 6, in <module>
    from ._scrublet import scrublet, filter_doublets
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/preprocessing/_scrublet.py", line 12, in <module>
    from snapatac2.tools._embedding import spectral
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/tools/__init__.py", line 6, in <module>
    from ._diff import marker_regions, diff_test
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/tools/_diff.py", line 5, in <module>
    from scipy.stats import chi2, norm, zscore
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/scipy/stats/__init__.py", line 605, in <module>
    from ._stats_py import *
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/scipy/stats/_stats_py.py", line 37, in <module>
    from scipy.spatial.distance import cdist
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/scipy/spatial/__init__.py", line 110, in <module>
    from ._kdtree import *
  File "/home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/scipy/spatial/_kdtree.py", line 4, in <module>
    from ._ckdtree import cKDTree, cKDTreeNode
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /home/hl737/.conda/envs/ds_notebook/lib/python3.12/site-packages/scipy/spatial/_ckdtree.cpython-312-x86_64-linux-gnu.so)
  0%|          | 0/8 [00:01<?, ?it/s]
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
File <timed eval>:1

File ~/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/tools/_call_peaks.py:155, in macs3(adata, groupby, qvalue, replicate, replicate_qvalue, max_frag_size, selections, nolambda, shift, extsize, min_len, blacklist, key_added, tempdir, inplace, n_jobs)
    152     return _snapatac2.find_reproducible_peaks(merged, others, blacklist)
    154 logging.info("Calling peaks...")
--> 155 peaks = _par_map(_call_peaks, [(x,) for x in fragments.values()], n_jobs)
    156 peaks = {k: v for k, v in zip(fragments.keys(), peaks)}
    157 if inplace:

File ~/.conda/envs/ds_notebook/lib/python3.12/site-packages/snapatac2/tools/_call_peaks.py:221, in _par_map(mapper, args, nprocs)
    219 while len(jobs) > 0:
    220     if any(map(lambda p: not p.is_alive(), procs)):
--> 221         raise RuntimeError("Some worker process has died unexpectedly.")
    223     remaining = []
    224     for i, job in jobs:

RuntimeError: Some worker process has died unexpectedly.

Snap version 2.6.0

Thank you in advance!

Start with snapatac2/tools/_call_peaks.py, especially macs3 and _par_map, and reproduce the reported call in the stated Python 3.12 environment. Trace how the worker failure becomes the generic RuntimeError and verify that the underlying import failure is surfaced clearly; no specific test file is named in the issue.