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YY-TMU / InPACT

A computational method designed to identify and quantify IPA sites via the examination of contextual sequence patterns and RNA-seq reads alignment.
MIT License
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FileNotFoundError: [Errno 2] No such file or directory: 'xxxxxxx/0.data_prepare #2

Open CTLife opened 6 months ago

CTLife commented 6 months ago

can not run InPACT:

InPACT -i ../0_BAM.2PASS/Input/mRNA_SRR8462062_GSM3572799_NA18498_Input.bam -a hg38.109.20211119.ncbiRefSeq.gtf -s InPACT_polyAsites.hg38.saf -P 8 -paired False

2024.03.30 15:26 Start ../0_BAM.2PASS/Input/mRNA_SRR8462062_GSM3572799_NA18498_Input.bam Prepare annotation files 2024-03-30 15:26: #########################Start : Date preparation######################### Traceback (most recent call last): File "/home/yp/.conda/envs/InPACT/bin/InPACT_annotation_prepare", line 335, in createDir(save_dir) File "/home/yp/.conda/envs/InPACT/bin/InPACT_annotation_prepare", line 26, in createDir os.mkdir(dir_file) FileNotFoundError: [Errno 2] No such file or directory: 'mRNA_SRR8462062_GSM3572799_NA18498_Input/0.data_prepare'

CTLife commented 6 months ago

I created folder mRNA_SRR8462062_GSM3572799_NA18498_Input, no this error.

But generated new error: Build model 2024-03-30 15:49: #########################Start : Training model######################### 2024-03-30 15:49: Parameters: 2024-03-30 15:49: Namespace(random_seed=888, sample_dir='mRNA_SRR8462062_GSM3572799_NA18498_Input', save_composite_model='composite.terminal.exon.model.pkl', save_dir='read_model', save_skip_model='skip.terminal.exon.model.pkl', train_fraction=0.8) 2024-03-30 15:49: ------------------------------ 2024-03-30 15:49: Processing skip... 2024-03-30 15:49: Test number : 798 2024-03-30 15:49: Rest number : 10157 Traceback (most recent call last): File "/home/yp/.conda/envs/InPACT/bin/InPACT_read_train_model", line 219, in ml_skip = buildModel(rt_rest_skip,random_seed) File "/home/yp/.conda/envs/InPACT/bin/InPACT_read_train_model", line 91, in buildModel ml.fit(rt_train_x,rt_train_y) File "/home/yp/.conda/envs/InPACT/lib/python3.8/site-packages/imblearn/ensemble/_bagging.py", line 321, in fit return self._fit(X, y, self.max_samples, sample_weight=None) File "/home/yp/.conda/envs/InPACT/lib/python3.8/site-packages/sklearn/ensemble/_bagging.py", line 337, in _fit max_features = self.max_features * self.n_featuresin AttributeError: 'BalancedBaggingClassifier' object has no attribute 'n_featuresin'

liuxc1995 commented 6 months ago

Hi, Thanks for your question. We have updated the InPACT script to automatically create the required directory, addressing the first question. Regarding the second question, it may be related to the scikit-learn package. Our tests with scikit-learn version 0.24.2 didn't show any issues. Please try reinstalling InPACT to address these concerns. Thank you, Liu