MicrobeLab
AttributeError: module 'tensorflow' has no attribute 'logging'. Did you mean: '_logging'? - issue while creating tfrec
I am trying to convert my reference fasta to TFrec file for training, following instructions on: https://github.com/MicrobeLab/DeepMicrobes/blob/master/document/tfrecord.md
It is able to shuffle the sequences, split but when the conversion starts I get this error. Could you please help me in this regard?
- Shuffling sequences for training... (echo -n ">"; cat <&0) | sed "s/^>/\x0>/" ======================================
- Splitting input to 20480000 sequences per file...
======================================
3. Converting to TFRecord...
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 119.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 585.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 631.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 632.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 633.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 666.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 1541.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 1547.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at
/DeepMicrobes/DeepMicrobes/bin/parallel line 1553.
(Maybe you should just omit the defined()?)
2023-12-11 10:10:56.981597: I external/local_tsl/tsl/cuda/cudart_stub.cc:31] Could not find cuda drivers on your machine, GPU will not be used.
2023-12-11 10:10:57.033642: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2023-12-11 10:10:57.033709: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2023-12-11 10:10:57.035517: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2023-12-11 10:10:57.045672: I external/local_tsl/tsl/cuda/cudart_stub.cc:31] Could not find cuda drivers on your machine, GPU will not be used.
2023-12-11 10:10:57.045963: 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.
2023-12-11 10:11:02.224734: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Traceback (most recent call last):
File "/DeepMicrobes/DeepMicrobes/scripts/seq2tfrec_kmer.py", line 239, in
In TensorFlow 2.0, the tf.logging module has been removed in favor of the open-source absl-py. To set the logging verbosity in TensorFlow 2.0 and later, you can use the absl logging methods:
import absl.logging absl.logging.set_verbosity(absl.logging.INFO)
The code was written in TF1. You could either modify the code accordingly or just remove the line of code.
