thread '<unnamed>' panicked at /root/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyanndata-0.2.1/src/anndata.rs:36:60:

[Susan920715]

Discussed in https://github.com/kaizhang/SnapATAC2/discussions/229

^{Originally posted by Susan920715 February 2, 2024} hello，everyone! when I run snap.pp.filter_cells(adi_adatas, min_tsse=7,n_jobs=1) It always makes the following error,,how can I solve it? thanyou very much

25%|██▌       | 1/4 [00:05<00:16,  5.54s/it]thread '<unnamed>' panicked at /root/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyanndata-0.2.1/src/anndata.rs:36:60:
called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 7294 to 12257
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Process SpawnPoolWorker-81:
Traceback (most recent call last):
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 315, in _bootstrap
    self.run()
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/snapatac2/_utils.py", line 30, in _func
    adata = internal.read(x[1])
pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 7294 to 12257
thread '<unnamed>' panicked at /root/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyanndata-0.2.1/src/anndata.rs:36:60:
called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 4716 to 6140
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Process SpawnPoolWorker-82:
Traceback (most recent call last):
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 315, in _bootstrap
    self.run()
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/snapatac2/_utils.py", line 30, in _func
    adata = internal.read(x[1])
pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 4716 to 6140
thread '<unnamed>' panicked at /root/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyanndata-0.2.1/src/anndata.rs:36:60:
called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 5137 to 9573
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Process SpawnPoolWorker-83:
Traceback (most recent call last):
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 315, in _bootstrap
    self.run()
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/multiprocess/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/data/wangjiamin/miniconda3/envs/py3.9/lib/python3.9/site-packages/snapatac2/_utils.py", line 30, in _func
    adata = internal.read(x[1])
pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: dimension cannot be changed from 5137 to 9573

[kaizhang]

Could you please share the h5ad file with me, so that I can try to reproduce the issue?

[Susan920715]

Of course, when I tried to solve this problem yesterday, I found that adi_adatas was closed after running this command. I guessed that the file was damaged due to force majeure when running this command. When I deleted the file and ran it again, it did not report this error. However, this problem often occurs, it seems that the previous run will stall, and the problem will occur when it is re-run, and adatas will accidentally closed.