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eliza-m / NLRexpress

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ValueError: Input contains NaN, infinity or a value too large for dtype('float64') #1

Open polchan opened 1 year ago

polchan commented 1 year ago

Hi! Eliza. I have more than 100 NLR sequences, so I downloaded this code. But I met some errors during operations, this is my error code:

30/11/2022 12:17:55: ############ NLRexpress started ############ 30/11/2022 12:17:55: Input FASTA: CNLA_part_1.fasta 30/11/2022 12:17:55: Checking FASTA file - started 30/11/2022 12:17:55: Checking FASTA file - done 30/11/2022 12:17:55: Running JackHMMER - started 30/11/2022 13:51:46: Running JackHMMER - done 30/11/2022 13:51:46: Preparing features: Parsing HMM profile - started 30/11/2022 13:51:50: Running CCexpress : started 30/11/2022 13:51:50: Preparing features: NN input for motif extEDVID started 30/11/2022 13:51:52: Preparing features: NN input for motif extEDVID done Traceback (most recent call last): File "/ngsproject/bcguo/tools/NLRexpress/nlrexpress.py", line 200, in predict() File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(args, kwargs) File "/ngsproject/bcguo/tools/NLRexpress/nlrexpress.py", line 111, in predict results[p] = CCexpress.predictors[p].model.predict_proba( X ) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/neural_network/_multilayer_perceptron.py", line 1119, in predict_proba y_pred = self._forward_pass_fast(X) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/neural_network/_multilayer_perceptron.py", line 134, in _forward_pass_fast X = self._validate_data(X, accept_sparse=['csr', 'csc'], reset=False) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/base.py", line 421, in _validate_data X = check_array(X, check_params) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/utils/validation.py", line 63, in inner_f return f(*args, **kwargs) File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/utils/validation.py", line 720, in check_array _assert_all_finite(array, File "/ngsproject/bcguo/miniconda3/envs/nlrexpress/lib/python3.9/site-packages/sklearn/utils/validation.py", line 103, in _assert_all_finite raise ValueError( ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

Can you help solve this problem? Thanks

eliza-m commented 1 year ago

Hi,

Thank you for noticing this ! Could you please send me an input example that generated the error, to try to reproduce it ? (my address: elizamartinc{at}yahoo.com) Also, does the input example from '/sample/input/zar1_rpp1.fa' yields the same error ? Thank you !

Best, Eliza

polchan commented 1 year ago

Ok, I have sent mail to you.