可能是 转换后的兼容性问题,或者你看看saw convert转换过程有没有报错信息,是不是文件不完整;
python3 $scripts//scanpy_st_qc.py \ --h5ad ../02.convert/benihoppe_flower_S1.bin50.S1.h5ad \ --pt_size_factor 10 \ --image_scale lowres -p benihoppe_flower_S1 \ --slide_name benihoppe_flower_S1 -o benihoppe_flower_S1 \ --metadata_col_name SampleID \ --metadata_value benihoppe_flower_S1 \ --nGene_min 0 --min_spots 0
运行这条命令时出现的报错,../02.convert/benihoppe_flower_S1.bin50.S1.h5ad 我一个芯片上有三个样本这个是我其中一个样本,出现以下报错
[root@bfdc7cfb3afc 20:42:09 /work/STOmics/02.scanpy_data_qc]# python3 $scripts//scanpy_st_qc.py --h5ad ../02.convert/benihoppe_flower_S1.bin50.S1.h5ad \
--pt_size_factor 10 \
--image_scale lowres -p benihoppe_flower_S1 \
--slide_name benihoppe_flower_S1 -o benihoppe_flower_S1 \
--metadata_col_name SampleID \
--metadata_value benihoppe_flower_S1 \
--nGene_min 0 --min_spots 0
Namespace(count=None, sep='\t', data_dir=None, gene_column=2, h5ad='../02.convert/benihoppe_flower_S1.bin50.S1.h5ad', h5=None, slide_name='benihoppe_flower_S1', transpose=False, image_dir=None, image_scale='lowres', keep_spot_on_tissue=False, metadata=None, metadata_col_name=['SampleID'], metadata_value=['benihoppe_flower_S1'], nGene_max=None, nGene_min=0, nUMI_min=None, nUMI_max=None, min_spots=0, percent_mito=None, mito_gene_pattern=None, log10GenesPerUMI=None, percent_hb=None, hb_gene_pattern=None, percent_ribo=None, ribo_gene_pattern=None, percent_pt=None, pt_gene_pattern=None, shape='circle', pt_size_factor=10.0, spot_diameters=None, dpi=600, height=5, width=6, outdir='benihoppe_flower_S1', prefix='benihoppe_flower_S1')
/share/biosoft/python/Python3/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.
warnings.warn(
/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
warnings.warn(msg, FutureWarning)
Traceback (most recent call last):
File "/work/scripts///scanpy_st_qc.py", line 254, in <module>
adata = sc.read_h5ad(args.h5ad)
File "/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 260, in read_h5ad
adata = read_dispatched(f, callback=callback)
File "/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/experimental/_dispatch_io.py", line 42, in read_dispatched
return reader.read_elem(elem)
File "/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/_io/utils.py", line 213, in func_wrapper
return func(*args, **kwargs)
File "/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/_io/specs/registry.py", line 281, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
File "/share/biosoft/python/Python3/lib/python3.10/site-packages/anndata/_io/h5ad.py", line 240, in callback
return AnnData(
TypeError: AnnData.__init__() got an unexpected keyword argument 'work'
Error raised while reading key '' of <class 'h5py._hl.files.File'> from /