songliVT
commented
1 year ago Can you find this file in your directory? All_model.h5
On Fri, Apr 7, 2023 at 5:12 AM JunHe0831 @.***> wrote:
Hi,
When I use DeepTE.py, I meet an error like this : Using TensorFlow backend. WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3976: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:131: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:133: The name tf.placeholder_with_default is deprecated. Please use tf.compat.v1.placeholder_with_default instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version. Instructions for updating: Please use rate instead of keep_prob. Rate should be set to rate = 1 - keep_prob. WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.
2023-04-07 13:09:48.069590: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2023-04-07 13:09:48.107062: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2394370000 Hz 2023-04-07 13:09:48.111610: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5646dac61040 executing computations on platform Host. Devices: 2023-04-07 13:09:48.111668: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): , 2023-04-07 13:09:48.115493: I tensorflow/stream_executor/platform/default/dso_loader.cc:53] Could not dlopen library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /pub/software/root/lib 2023-04-07 13:09:48.115524: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303) 2023-04-07 13:09:48.115561: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (gs92): /proc/driver/nvidia/version does not exist 2023-04-07 13:09:48.168871: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set. If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU. To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile. WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/tensorflow/python/ops/math_grad.py:1250: add_dispatch_support..wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.where in 2.0, which has the same broadcast rule as np.where start time is 1680844187.1468675 Step1: transfer fasta data to CNN input data Step2: classify TEs Step2: 2) domain information is not exist Traceback (most recent call last): File "/pub/software/DeepTE/DeepTE.py", line 274, in main() File "/pub/software/DeepTE/DeepTE.py", line 249, in main pipeline_no_m.classify_pipeline(model_dir, input_CNN_data_file, temp_store_opt_dir, sp_type,te_fam,prop_thr) File "/pub/software/DeepTE/scripts/DeepTE_pipeline_no_modification.py", line 339, in classify_pipeline predict_te(model_file_dic[model_name], model_name, x_all_test_list, y_all_test_nm_list,input_spe_type,y_all_test_nm_list,prop_thr) File "/pub/software/DeepTE/scripts/DeepTE_pipeline_no_modification.py", line 210, in predict_te model = load_model(model) File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 419, in load_model model = _deserialize_model(f, custom_objects, compile) File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 323, in _deserialize_model optimizer_weight_names] File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 322, in optimizer_weight_values = [optimizer_weights_group[n] for n in File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/utils/io_utils.py", line 285, in getitem val = np.asarray(val) File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/numpy/core/numeric.py", line 538, in asarray return array(a, dtype, copy=False, order=order) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 772, in array self.read_direct(arr) File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 733, in read_direct self.id.read(mspace, fspace, dest, dxpl=self._dxpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5d.pyx", line 181, in h5py.h5d.DatasetID.read File "h5py/_proxy.pyx", line 130, in h5py._proxy.dset_rw File "h5py/_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread OSError: Can't read data (file read failed: time = Fri Apr 7 13:09:50 2023 , filename = '/pub/software/DeepTE/Model_dir/Plants_model/All_model.h5', file descriptor = 5, errno = 5, error message = 'Input/output error', buf = 0x7fc7029de548, total read size = 88676040, bytes this sub-read = 88676040, bytes actually read = 18446744073709551615, offset = 0) I got the 'opt_input_CNN_data.txt' file but didn`t got .fasta results.
— Reply to this email directly, view it on GitHub https://github.com/LiLabAtVT/DeepTE/issues/23, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEEENWDYJ55F7WTZ742VSDW77LARANCNFSM6AAAAAAWWL4TMM . You are receiving this because you are subscribed to this thread.Message ID: @.***>
-- Associate Professor in Plant Genomics and Bioinformatics School of Plant and Environmental Sciences Virginia Polytechnic Institute and State University
JunHe0831
linshengnan09
Hi,
When I use DeepTE.py, I meet an error like this : Using TensorFlow backend. WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3976: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:131: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:133: The name tf.placeholder_with_default is deprecated. Please use tf.compat.v1.placeholder_with_default instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3445: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version. Instructions for updating: Please use
rateinstead ofkeep_prob. Rate should be set torate = 1 - keep_prob. WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.2023-04-07 13:09:48.069590: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2023-04-07 13:09:48.107062: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2394370000 Hz 2023-04-07 13:09:48.111610: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5646dac61040 executing computations on platform Host. Devices: 2023-04-07 13:09:48.111668: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0):,
2023-04-07 13:09:48.115493: I tensorflow/stream_executor/platform/default/dso_loader.cc:53] Could not dlopen library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /pub/software/root/lib
2023-04-07 13:09:48.115524: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303)
2023-04-07 13:09:48.115561: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (gs92): /proc/driver/nvidia/version does not exist
2023-04-07 13:09:48.168871: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set. If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU. To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.
WARNING:tensorflow:From /pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/tensorflow/python/ops/math_grad.py:1250: add_dispatch_support..wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.where in 2.0, which has the same broadcast rule as np.where
start time is 1680844187.1468675
Step1: transfer fasta data to CNN input data
Step2: classify TEs
Step2: 2) domain information is not exist
Traceback (most recent call last):
File "/pub/software/DeepTE/DeepTE.py", line 274, in
main()
File "/pub/software/DeepTE/DeepTE.py", line 249, in main
pipeline_no_m.classify_pipeline(model_dir, input_CNN_data_file, temp_store_opt_dir, sp_type,te_fam,prop_thr)
File "/pub/software/DeepTE/scripts/DeepTE_pipeline_no_modification.py", line 339, in classify_pipeline
predict_te(model_file_dic[model_name], model_name, x_all_test_list, y_all_test_nm_list,input_spe_type,y_all_test_nm_list,prop_thr)
File "/pub/software/DeepTE/scripts/DeepTE_pipeline_no_modification.py", line 210, in predict_te
model = load_model(model)
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 419, in load_model
model = _deserialize_model(f, custom_objects, compile)
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 323, in _deserialize_model
optimizer_weight_names]
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/engine/saving.py", line 322, in
optimizer_weight_values = [optimizer_weights_group[n] for n in
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/keras/utils/io_utils.py", line 285, in getitem
val = np.asarray(val)
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/numpy/core/numeric.py", line 538, in asarray
return array(a, dtype, copy=False, order=order)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 772, in array
self.read_direct(arr)
File "/pub/anaconda3/envs/DeepTE/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 733, in read_direct
self.id.read(mspace, fspace, dest, dxpl=self._dxpl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5d.pyx", line 181, in h5py.h5d.DatasetID.read
File "h5py/_proxy.pyx", line 130, in h5py._proxy.dset_rw
File "h5py/_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread
OSError: Can't read data (file read failed: time = Fri Apr 7 13:09:50 2023
, filename = '/pub/software/DeepTE/Model_dir/Plants_model/All_model.h5', file descriptor = 5, errno = 5, error message = 'Input/output error', buf = 0x7fc7029de548, total read size = 88676040, bytes this sub-read = 88676040, bytes actually read = 18446744073709551615, offset = 0)
I got the 'opt_input_CNN_data.txt' file but didn`t got .fasta results.