Problem running scATAC-seq with taiji #43
Description
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