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View Code? Open in Web Editor NEWDeepLncCTCF for identification and analysis of consensus RNA motifs binding to the genome regulator CTCF
DeepLncCTCF for identification and analysis of consensus RNA motifs binding to the genome regulator CTCF
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
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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