Open ordabayevy opened 4 months ago
There was a similar error before:
File "/mnt/disks/dev/repos/cellarium-ml/cellarium/ml/data/fileio.py", line 38, in read_h5ad_gcs
return read_h5ad(f)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 261, in read_h5ad
adata = read_dispatched(f, callback=callback)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/experimental/_dispatch_io.py", line 48, in read_dispatched
return reader.read_elem(elem)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/utils.py", line 207, in func_wrapper
return func(*args, **kwargs)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 256, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 242, in callback
**{
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 245, in <dictcomp>
k: read_dispatched(elem[k], callback)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/experimental/_dispatch_io.py", line 48, in read_dispatched
return reader.read_elem(elem)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/utils.py", line 207, in func_wrapper
return func(*args, **kwargs)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 256, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 259, in callback
return func(elem)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 304, in read_mapping
return {k: _reader.read_elem(v) for k, v in elem.items()}
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 304, in <dictcomp>
return {k: _reader.read_elem(v) for k, v in elem.items()}
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/utils.py", line 207, in func_wrapper
return func(*args, **kwargs)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 256, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 259, in callback
return func(elem)
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/anndata/_io/specs/methods.py", line 378, in read_array
return elem[()]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/yordabay/anaconda3/envs/cellarium/lib/python3.10/site-packages/h5py/_hl/dataset.py", line 841, in __getitem__
self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5d.pyx", line 242, in h5py.h5d.DatasetID.read
File "h5py/_proxy.pyx", line 113, in h5py._proxy.dset_rw
OSError: Can't synchronously read data (wrong B-tree signature)
Error raised while reading key 'measured_genes_mask' of <class 'h5py._hl.dataset.Dataset'> from /layers
This error happens when training multiple models on the same dataset (google bucket).