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I want to predict the TF binding sites using your example peak file. The reference genome is hg38, and the bed file is fox01_peaks.bed.
After processing peak file using command "python processing_peaks.py --name fox01_peaks.bed --peak_flank 50", I started to train the model. but i got an error message below.
python train.py --start_index 0 --end_index 1 --peak_flank 50 --network CNN --feature_format Seq Sequence length: 101 Dataset: fox01_peaks_encode Traceback (most recent call last): File "train.py", line 163, in <module> tf.app.run() File "/home/zhenyingLab/zhukangli/.conda/envs/desso/lib/python2.7/site-packages/tensorflow/python/platform/app.py", line 48, in run _sys.exit(main(_sys.argv[:1] + flags_passthrough)) File "train.py", line 68, in main util.load_data_encode(PATH_ENCODE + "/" + train_data_name + "_AC.seq.gz", peak_coor, train_data_name, path_curr_data, "train", DNA_SHAPE, peak_flank, back_grou) File "/storage/zhenyingLab/zhukangli/software/DESSO-master/data/libs/util.py", line 138, in load_data_encode sequences = np.concatenate((sequences, seq_shuffle), axis = 0) ValueError: all the input array dimensions except for the concatenation axis must match exactly
Any help or guidance would be greatly appreciated!
Thank you!
kangli zhu
The text was updated successfully, but these errors were encountered:
Hello,
I want to predict the TF binding sites using your example peak file. The reference genome is hg38, and the bed file is fox01_peaks.bed.
After processing peak file using command "python processing_peaks.py --name fox01_peaks.bed --peak_flank 50", I started to train the model. but i got an error message below.
python train.py --start_index 0 --end_index 1 --peak_flank 50 --network CNN --feature_format Seq Sequence length: 101 Dataset: fox01_peaks_encode Traceback (most recent call last): File "train.py", line 163, in <module> tf.app.run() File "/home/zhenyingLab/zhukangli/.conda/envs/desso/lib/python2.7/site-packages/tensorflow/python/platform/app.py", line 48, in run _sys.exit(main(_sys.argv[:1] + flags_passthrough)) File "train.py", line 68, in main util.load_data_encode(PATH_ENCODE + "/" + train_data_name + "_AC.seq.gz", peak_coor, train_data_name, path_curr_data, "train", DNA_SHAPE, peak_flank, back_grou) File "/storage/zhenyingLab/zhukangli/software/DESSO-master/data/libs/util.py", line 138, in load_data_encode sequences = np.concatenate((sequences, seq_shuffle), axis = 0) ValueError: all the input array dimensions except for the concatenation axis must match exactly
Any help or guidance would be greatly appreciated!
Thank you!
kangli zhu
The text was updated successfully, but these errors were encountered: