Open monoplasty opened 1 year ago
When I executed the Simulated data from scRNA data code of the SimulatedData.ipynb file, the following error occurred:
OSError Traceback (most recent call last) Cell In[7], line 4 1 scRNADir1 = 'Brain_10X' 2 scRNADir2 = 'Brain_Smart-seq' ----> 4 generate_dataset_data(scRNADir1, scRNADir2, celltype_key = 'celltype_final',reverse = False) 5 generate_dataset_data(scRNADir1, scRNADir2, celltype_key = 'celltype_final',reverse = True) Cell In[5], line 2, in generate_dataset_data(scRNADir1, scRNADir2, celltype_key, reverse) 1 def generate_dataset_data(scRNADir1, scRNADir2, celltype_key,reverse = False): ----> 2 scrna, spatial = check_dataset(scRNADir1, scRNADir2, top_genes=200, plot=False,reverse=reverse,check=False) 3 if not reverse: 4 output_dir = scRNADir1 Cell In[3], line 37, in check_dataset(scRNADir1, scRNADir2, top_genes, plot, reverse, check) 34 assert len(celltype_meta_1['celltype_final'][celltype_meta_1['celltype_final'] != 'Not_specific'].unique()) == len(overlaped_celltype), data_ident_1+': unique celltype length dont match.' 35 assert len(celltype_meta_2['celltype_final'][celltype_meta_2['celltype_final'] != 'Not_specific'].unique()) == len(overlaped_celltype), data_ident_2+': unique celltype length dont match.' ---> 37 data_1 = sc.read_h5ad(scRNADir1 + '/scRNA.h5ad') 38 data_2 = sc.read_h5ad(scRNADir2 + '/scRNA.h5ad') 40 data_1 = check_adata(data_1, os.path.join(scRNADir1, 'Processed_scRNA.h5ad')) File ~/miniconda3/envs/py38/lib/python3.8/site-packages/anndata/_io/h5ad.py:219, in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size) 211 raise NotImplementedError( 212 "Currently only `X` and `raw/X` can be read as sparse." 213 ) 215 rdasp = partial( 216 read_dense_as_sparse, sparse_format=as_sparse_fmt, axis_chunk=chunk_size 217 ) --> 219 with h5py.File(filename, "r") as f: 221 def callback(func, elem_name: str, elem, iospec): 222 if iospec.encoding_type == "anndata" or elem_name.endswith("/"): File ~/miniconda3/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py:424, in File.__init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, **kwds) 422 with phil: 423 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, **kwds) --> 424 fid = make_fid(name, mode, userblock_size, 425 fapl, fcpl=make_fcpl(track_order=track_order, fs_strategy=fs_strategy, 426 fs_persist=fs_persist, fs_threshold=fs_threshold), 427 swmr=swmr) 429 if isinstance(libver, tuple): 430 self._libver = libver File ~/miniconda3/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py:190, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr) 188 if swmr and swmr_support: 189 flags |= h5f.ACC_SWMR_READ --> 190 fid = h5f.open(name, flags, fapl=fapl) 191 elif mode == 'r+': 192 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper() File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper() File h5py/h5f.pyx:96, in h5py.h5f.open() OSError: Unable to open file (truncated file: eof = 3001450496, sblock->base_addr = 0, stored_eof = 5047473549)
I searched for similar issues and got the answer that the original file is corrupted. my env:
Package Version ------------------- ------- anndata 0.9.1 asttokens 2.0.5 backcall 0.2.0 blosc2 2.0.0 comm 0.1.2 contourpy 1.0.7 cycler 0.11.0 Cython 0.29.34 debugpy 1.5.1 decorator 5.1.1 dunamai 1.16.0 executing 0.8.3 fonttools 4.39.3 get_version 3.5.4 h5py 3.1.0 importlib-metadata 6.0.0 importlib-resources 5.12.0 ipykernel 6.19.2 ipython 8.12.0 jedi 0.18.1 joblib 1.2.0 jupyter_client 8.1.0 jupyter_core 5.3.0 kiwisolver 1.4.4 legacy-api-wrap 1.2 llvmlite 0.40.0 matplotlib 3.3.4 matplotlib-inline 0.1.6 msgpack 1.0.5 natsort 8.3.1 nest-asyncio 1.5.6 networkx 3.1 numba 0.57.0 numexpr 2.8.4 numpy 1.24.3 packaging 23.0 pandas 1.1.5 parso 0.8.3 patsy 0.5.3 pexpect 4.8.0 pickleshare 0.7.5 Pillow 9.5.0 pip 23.0.1 platformdirs 2.5.2 prompt-toolkit 3.0.36 psutil 5.9.0 ptyprocess 0.7.0 pure-eval 0.2.2 py-cpuinfo 9.0.0 Pygments 2.15.1 pynndescent 0.5.10 pyparsing 3.0.9 python-dateutil 2.8.2 pytz 2023.3 pyzmq 25.0.2 scanpy 1.7.2 scikit-learn 1.2.2 scipy 1.10.1 seaborn 0.12.2 setuptools 66.0.0 sinfo 0.3.4 six 1.16.0 stack-data 0.2.0 statsmodels 0.14.0 stdlib-list 0.8.0 tables 3.8.0 threadpoolctl 3.1.0 tornado 6.2 tqdm 4.65.0 traitlets 5.7.1 typing_extensions 4.5.0 tzdata 2023.3 umap-learn 0.5.3 wcwidth 0.2.5 wheel 0.38.4 zipp 3.11.0
When I executed the Simulated data from scRNA data code of the SimulatedData.ipynb file, the following error occurred:
I searched for similar issues and got the answer that the original file is corrupted. my env: