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Problem running scATAC-seq with taiji #43

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youjingyuan opened this issue Nov 12, 2023 · 0 comments
Open

Problem running scATAC-seq with taiji #43

youjingyuan opened this issue Nov 12, 2023 · 0 comments

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@youjingyuan
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Hi,

I am running the QC part of taiji and encountered the following error:

[INFO][11-12 23:23] SCATAC_Pre_Cluster(7e8b..): Running ...
Read Data
Use jaccard distance
Compute similarity matrix
Traceback (most recent call last):
File "/home/jingyuan/.local/bin/taiji-utils", line 8, in
sys.exit(main())
^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/init.py", line 151, in main
args.func(args)
File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/init.py", line 12, in reduce
spectral(args)
File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 38, in spectral
res = Spectral(mat, n_dim=args.dim, distance=args.distance).coordinates[:, 1:]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 62, in init
self.normalizer = Normalizer(jm, self.coverage)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 101, in init
self.model = LinearRegression().fit(X, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 1152, in wrapper
return fit_method(estimator, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/linear_model/_base.py", line 678, in fit
X, y = self.validate_data(
^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 622, in validate_data
X, y = check_X_y(X, y, **check_params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 1146, in check_X_y
X = check_array(
^^^^^^^^^^^^
File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 751, in check_array
raise TypeError(
TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html
[ERROR][11-12 23:23] SCATAC_Pre_Cluster(7e8b..) Failed:
Ran commands:
taiji-utils reduce /scratch/42548086/tmp_dir-e61da8f959579a79/forebrain_E11.5_rep1_filt.mat.gz /scratch/42548086/tmp_dir-e61da8f959579a79/forebrain_E11.5_rep1_spectral.tsv.gz
which taiji-utils

  Exception: error running: taiji-utils reduce /scratch/42548086/tmp_dir_-e61da8f959579a79/forebrain_E11.5_rep1_filt.mat.gz /scratch/42548086/tmp_dir_-e61da8f959579a79/forebrain_E11.5_rep1_spectral.tsv.gz
  exit status: 1
  stderr: Traceback (most recent call last):
    File "/home/jingyuan/.local/bin/taiji-utils", line 8, in <module>
    sys.exit(main())
  ^^^^^^
    File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 151, in main
  args.func(args)
  File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 12, in reduce
  spectral(args)
  File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 38, in spectral
  res = Spectral(mat, n_dim=args.dim, distance=args.distance).coordinates[:, 1:]
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 62, in __init__
  self.normalizer = Normalizer(jm, self.coverage)
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 101, in __init__
  self.model = LinearRegression().fit(X, y)
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 1152, in wrapper
  return fit_method(estimator, *args, **kwargs)
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/linear_model/_base.py", line 678, in fit
  X, y = self._validate_data(
    ^^^^^^^^^^^^^^^^^^^^
      File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 622, in _validate_data
    X, y = check_X_y(X, y, **check_params)
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 1146, in check_X_y
    X = check_array(
      ^^^^^^^^^^^^
        File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 751, in check_array
      raise TypeError(
        TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html
        
        CallStack (from HasCallStack):
          error, called at src/Control/Workflow/Interpreter/Exec.hs:146:37 in SciFlow-0.8.0-IRKsT2ba9M716PeGlwt2FT:Control.Workflow.Interpreter.Exec
        [INFO][11-12 23:23] SCATAC_Pre_Cluster(0215..): Running ...
        Read Data
        Use jaccard distance
        Compute similarity matrix
        Traceback (most recent call last):
          File "/home/jingyuan/.local/bin/taiji-utils", line 8, in <module>
          sys.exit(main())
        ^^^^^^
          File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 151, in main
        args.func(args)
        File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 12, in reduce
        spectral(args)
        File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 38, in spectral
        res = Spectral(mat, n_dim=args.dim, distance=args.distance).coordinates[:, 1:]
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 62, in __init__
        self.normalizer = Normalizer(jm, self.coverage)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 101, in __init__
        self.model = LinearRegression().fit(X, y)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 1152, in wrapper
        return fit_method(estimator, *args, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/linear_model/_base.py", line 678, in fit
        X, y = self._validate_data(
          ^^^^^^^^^^^^^^^^^^^^
            File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 622, in _validate_data
          X, y = check_X_y(X, y, **check_params)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 1146, in check_X_y
          X = check_array(
            ^^^^^^^^^^^^
              File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 751, in check_array
            raise TypeError(
              TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html
              [ERROR][11-12 23:23] SCATAC_Pre_Cluster(0215..) Failed: 
                Ran commands: 
                taiji-utils reduce /scratch/42548086/tmp_dir_-72882c3eb78d8439/forebrain_P0_rep1_filt.mat.gz /scratch/42548086/tmp_dir_-72882c3eb78d8439/forebrain_P0_rep1_spectral.tsv.gz
              which taiji-utils
              
              Exception: error running: taiji-utils reduce /scratch/42548086/tmp_dir_-72882c3eb78d8439/forebrain_P0_rep1_filt.mat.gz /scratch/42548086/tmp_dir_-72882c3eb78d8439/forebrain_P0_rep1_spectral.tsv.gz
              exit status: 1
              stderr: Traceback (most recent call last):
                File "/home/jingyuan/.local/bin/taiji-utils", line 8, in <module>
                sys.exit(main())
              ^^^^^^
                File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 151, in main
              args.func(args)
              File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/__init__.py", line 12, in reduce
              spectral(args)
              File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 38, in spectral
              res = Spectral(mat, n_dim=args.dim, distance=args.distance).coordinates[:, 1:]
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 62, in __init__
              self.normalizer = Normalizer(jm, self.coverage)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/home/jingyuan/.local/lib/python3.11/site-packages/taiji_utils/Spectral.py", line 101, in __init__
              self.model = LinearRegression().fit(X, y)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 1152, in wrapper
              return fit_method(estimator, *args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/linear_model/_base.py", line 678, in fit
              X, y = self._validate_data(
                ^^^^^^^^^^^^^^^^^^^^
                  File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/base.py", line 622, in _validate_data
                X, y = check_X_y(X, y, **check_params)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 1146, in check_X_y
                X = check_array(
                  ^^^^^^^^^^^^
                    File "/home/jingyuan/.local/lib/python3.11/site-packages/sklearn/utils/validation.py", line 751, in check_array
                  raise TypeError(
                    TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html
                    
                    CallStack (from HasCallStack):
                      error, called at src/Control/Workflow/Interpreter/Exec.hs:146:37 in SciFlow-0.8.0-IRKsT2ba9M716PeGlwt2FT:Control.Workflow.Interpreter.Exec
                    [ERROR][11-12 23:23] Program exits with errors

It says that, "np.matrix is not supported. Please convert to a numpy array with np.asarray.". I am using python 3.11.4. Many thanks in advance!

Best,
JY
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