我已经按照安装步骤参考文档here.当我运行cellbender,我看到以下 * 错误 *,请检查并建议什么可能是正确的修复这里:
(CellBender) C:\Users\user12\Desktop\cellbender_test>cellbender remove-background --input C:\Users\user12\Desktop\feature_bc_matrix.h5 --output C:\Users\user12\Desktop\output.h5 --cuda --expected-cells 5000 --total-droplets-included 20000 --fpr 0.01 --epochs 150
Traceback (most recent call last):
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\Scripts\cellbender-script.py", line 33, in <module>
sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
File "c:\users\user12\desktop\cellbender_test\cellbender\cellbender\base_cli.py", line 91, in main
cli_dict = generate_cli_dictionary()
File "c:\users\user12\desktop\cellbender_test\cellbender\cellbender\base_cli.py", line 52, in generate_cli_dictionary
module_cli = importlib.import_module('.'.join(module_cli_str_list))
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\lib\importlib\__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "c:\users\user12\desktop\cellbender_test\cellbender\cellbender\remove_background\cli.py", line 4, in <module>
from cellbender.remove_background.data.dataset import SingleCellRNACountsDataset
File "c:\users\user12\desktop\cellbender_test\cellbender\cellbender\remove_background\data\dataset.py", line 10, in <module>
import anndata
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\lib\site-packages\anndata\__init__.py", line 7, in <module>
from ._core.anndata import AnnData
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\lib\site-packages\anndata\_core\anndata.py", line 17, in <module>
import h5py
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\lib\site-packages\h5py\__init__.py", line 33, in <module>
from . import version
File "C:\Users\user12\AppData\Local\anaconda3\envs\CellBender\lib\site-packages\h5py\version.py", line 15, in <module>
from . import h5 as _h5
File "h5py\h5.pyx", line 1, in init h5py.h5
ImportError: DLL load failed: The specified procedure could not be found.
我试着安装h5 py- 3.6.0和3.1.0,这些版本在我的情况下都不起作用。此外,我打印出导入路径并从 * h5 py * 复制相应的文件,仍然没有运气。
1条答案
按热度按时间cgfeq70w1#
当你同时使用pytables和h5 py时,这是一个令人恼火的事情。它们都使用HDF 5库/dll。当它们使用不同的版本时,你会得到错误消息。我的系统上也有同样的问题(所以我可以复制错误)。首先,检查系统上的版本。
检查h5 py的HDF 5版本:
检查pytables的HDF 5版本:
正如你所看到的,我在两个包之间有一个HDF 5库不匹配(h5 py的1.12.0和pytables的1.10.6)。我怀疑你是把h5 py作为pytorch的一部分。(它支持HDF 5文件。)解决方案是在pytorch中安装一个与h5 py具有相同HDF 5版本的pytables版本。