空间转录组质控-scanpy

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 /

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2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

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;


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gz_li

我要是整体分析完,再划分区域是不是就不会出现这个问题?

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