Hi Kevin
There was a bug when I tried to use 'scaden process':
INFO Scaling using log_min_max functions.py:65
Traceback (most recent call last):
File "/data/software/Python-3.8.5/bin/scaden", line 8, in
sys.exit(main())
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/main.py", line 48, in main
cli()
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/main.py", line 155, in process
processing(
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/process.py", line 35, in processing
preprocess_h5ad_data(raw_input_path=training_data,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/model/functions.py", line 67, in preprocess_h5ad_data
raw_input.X = sample_scaling(raw_input.X, scaling_option)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/model/functions.py", line 42, in sample_scaling
x = mms.fit_transform(x.T).T
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/base.py", line 699, in fit_transform
return self.fit(X, **fit_params).transform(X)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/preprocessing/_data.py", line 363, in fit
return self.partial_fit(X, y)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/preprocessing/_data.py", line 396, in partial_fit
X = self._validate_data(X, reset=first_pass,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/base.py", line 421, in _validate_data
X = check_array(X, **check_params)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 63, in inner_f
return f(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 663, in check_array
_assert_all_finite(array,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 103, in _assert_all_finite
raise ValueError(
ValueError: Input contains infinity or a value too large for dtype('float32').
After that I checked the simulated data (data.h5ad) and found the 'inf' value in the simulated data.
May I have your suggestion on this issue? Thanks a lot!
Jianyu
Hi Kevin
There was a bug when I tried to use 'scaden process':
INFO Scaling using log_min_max functions.py:65
Traceback (most recent call last):
File "/data/software/Python-3.8.5/bin/scaden", line 8, in
sys.exit(main())
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/main.py", line 48, in main
cli()
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/main.py", line 155, in process
processing(
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/process.py", line 35, in processing
preprocess_h5ad_data(raw_input_path=training_data,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/model/functions.py", line 67, in preprocess_h5ad_data
raw_input.X = sample_scaling(raw_input.X, scaling_option)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/scaden/model/functions.py", line 42, in sample_scaling
x = mms.fit_transform(x.T).T
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/base.py", line 699, in fit_transform
return self.fit(X, **fit_params).transform(X)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/preprocessing/_data.py", line 363, in fit
return self.partial_fit(X, y)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/preprocessing/_data.py", line 396, in partial_fit
X = self._validate_data(X, reset=first_pass,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/base.py", line 421, in _validate_data
X = check_array(X, **check_params)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 63, in inner_f
return f(*args, **kwargs)
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 663, in check_array
_assert_all_finite(array,
File "/data/software/Python-3.8.5/lib/python3.8/site-packages/sklearn/utils/validation.py", line 103, in _assert_all_finite
raise ValueError(
ValueError: Input contains infinity or a value too large for dtype('float32').
After that I checked the simulated data (data.h5ad) and found the 'inf' value in the simulated data.
May I have your suggestion on this issue? Thanks a lot!
Jianyu