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deeplncctcf's Issues

No module named 'keras.layers.recurrent'

Hi DeepLnc-er,
i am running the tool on ubuntu machine but i still get this error message:
$ python prediction.py -f plat.fa -o prediction.txt 2023-03-31 10:40:28.121728: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-03-31 10:40:28.998611: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT 2023-03-31 10:40:29.706883: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected Traceback (most recent call last): File "prediction.py", line 4, in <module> from train import * File "/workspace/DeepLncCTCF/train.py", line 16, in <module> from keras.layers.recurrent import LSTM ModuleNotFoundError: No module named 'keras.layers.recurrent'

could you help?
thanks
TA

ValueError: could not broadcast input array from shape (4,675) into shape (4,201)

Dear all,
I am trying to use this interesting tool to predict CTCF binding to my lncRNA using:
python /prediction.py -f /Users/tali/Desktop/lncRNA_seqes.fa -o prediction.output
however, the tool throws out this error message:

2022-10-05 10:08:59.419265: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-10-05 10:09:01.960968: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
WARNING:tensorflow:Please fix your imports. Module tensorflow.python.training.tracking.base has been moved to tensorflow.python.trackable.base. The old module will be deleted in version 2.11.
Traceback (most recent call last):
  File "/prediction.py", line 36, in <module>
    main()
  File "/prediction.py", line 33, in main
    prediction(infile,outfile)
  File "/prediction.py", line 10, in prediction
    X,geneinfo = get_pred_data(infile)
  File /utils.py", line 91, in get_pred_data
    (seqmatrix, gene, rank) = get_seq_matrix(infile,seqmatrix,rank)
  File "/utils.py", line 48, in get_seq_matrix
    seqmatrix[rank] = seqcode
ValueError: could not broadcast input array from shape (4,675) into shape (4,201)

what might be went wrong?
Im using MacOS 12.2
thanks much
Tamer

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