Error in loading pre-trained data

Question

Error in loading pre-trained data

yingc123 opened this issue 5 years ago · comments

Hello,
when I run the code, I got error like following.
I've already downloaded the corresponding file and tensorflow.
Does anyone have the same problem and how to deal?

from avocado import Avocado
Using TensorFlow backend.
model = Avocado.load('avocado-chr19')
WARNING:tensorflow:From /home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
Traceback (most recent call last):
File "", line 1, in
File "/home/ying/Cluster/home/avocado/model.py", line 1030, in load
**d)
File "/home/ying/Cluster/home/avocado/model.py", line 231, in init
freeze_network=freeze_network)
File "/home/ying/Cluster/home/avocado/model.py", line 53, in build_model
genome_250bp = Flatten()(genome_250bp_embedding(genome_250bp_input))
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 431, in call
self.build(unpack_singleton(input_shapes))
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/layers/embeddings.py", line 109, in build
dtype=self.dtype)
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/legacy/interfaces.py", line 91, in wrapper
return func(*args, **kwargs)
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 249, in add_weight
weight = K.variable(initializer(shape),
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/initializers.py", line 112, in call
dtype=dtype, seed=self.seed)
File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py", line 4139, in random_uniform
dtype=dtype, seed=seed)
File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/random_ops.py", line 247, in random_uniform
rnd = gen_random_ops.random_uniform(shape, dtype, seed=seed1, seed2=seed2)
File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/gen_random_ops.py", line 777, in random_uniform
name=name)
File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 610, in _apply_op_helper
param_name=input_name)
File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 60, in _SatisfiesTypeConstraint
", ".join(dtypes.as_dtype(x).name for x in allowed_list)))
TypeError: Value passed to parameter 'shape' has DataType float32 not in list of allowed values: int32, int64

Jacob Schreiber · Answer 1 · Mon Apr 01 2019 23:06:10 GMT+0800 (China Standard Time)

That’s weird. Can you try using the Theano backend instead and see if that works?

…

On Mon, Apr 1, 2019 at 6:11 AM yingc123 ***@***.***> wrote: Hello, when I run the code, I got error like following. I've already downloaded the corresponding file and tensorflow. Does anyone have the same problem and how to deal? from avocado import Avocado Using TensorFlow backend. model = Avocado.load('avocado-chr19') WARNING:tensorflow:From /home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. Traceback (most recent call last): File "", line 1, in File "/home/ying/Cluster/home/avocado/model.py", line 1030, in load **d) File "/home/ying/Cluster/home/avocado/model.py", line 231, in *init* freeze_network=freeze_network) File "/home/ying/Cluster/home/avocado/model.py", line 53, in build_model genome_250bp = Flatten()(genome_250bp_embedding(genome_250bp_input)) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 431, in *call* self.build(unpack_singleton(input_shapes)) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/layers/embeddings.py", line 109, in build dtype=self.dtype) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/legacy/interfaces.py", line 91, in wrapper return func(*args, **kwargs) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 249, in add_weight weight = K.variable(initializer(shape), File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/initializers.py", line 112, in *call* dtype=dtype, seed=self.seed) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py", line 4139, in random_uniform dtype=dtype, seed=seed) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/random_ops.py", line 247, in random_uniform rnd = gen_random_ops.random_uniform(shape, dtype, seed=seed1, seed2=seed2) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/gen_random_ops.py", line 777, in random_uniform name=name) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 610, in _apply_op_helper param_name=input_name) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 60, in _SatisfiesTypeConstraint ", ".join(dtypes.as_dtype(x).name for x in allowed_list))) TypeError: Value passed to parameter 'shape' has DataType float32 not in list of allowed values: int32, int64 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADvEEBN6dmGZMGl-x0gncI73SEJ40TiQks5vcgVsgaJpZM4cVrbt> .

yingc123 · Answer 2 · Tue Apr 02 2019 14:55:02 GMT+0800 (China Standard Time)

Hello, It is fixed. Since I do not use GPU... Best wishes, Ying Chen

________________________________ 发件人: Jacob Schreiber <notifications@github.com> 发送时间: 2019年4月1日 17:06:11 收件人: jmschrei/avocado 抄送: Chen, Ying; Author 主题: Re: [jmschrei/avocado] Error in loading pre-trained data (#5) That’s weird. Can you try using the Theano backend instead and see if that works?

On Mon, Apr 1, 2019 at 6:11 AM yingc123 ***@***.***> wrote: Hello, when I run the code, I got error like following. I've already downloaded the corresponding file and tensorflow. Does anyone have the same problem and how to deal? from avocado import Avocado Using TensorFlow backend. model = Avocado.load('avocado-chr19') WARNING:tensorflow:From /home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. Traceback (most recent call last): File "", line 1, in File "/home/ying/Cluster/home/avocado/model.py", line 1030, in load **d) File "/home/ying/Cluster/home/avocado/model.py", line 231, in *init* freeze_network=freeze_network) File "/home/ying/Cluster/home/avocado/model.py", line 53, in build_model genome_250bp = Flatten()(genome_250bp_embedding(genome_250bp_input)) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 431, in *call* self.build(unpack_singleton(input_shapes)) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/layers/embeddings.py", line 109, in build dtype=self.dtype) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/legacy/interfaces.py", line 91, in wrapper return func(*args, **kwargs) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/engine/base_layer.py", line 249, in add_weight weight = K.variable(initializer(shape), File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/initializers.py", line 112, in *call* dtype=dtype, seed=self.seed) File "/home/ying/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py", line 4139, in random_uniform dtype=dtype, seed=seed) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/random_ops.py", line 247, in random_uniform rnd = gen_random_ops.random_uniform(shape, dtype, seed=seed1, seed2=seed2) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/ops/gen_random_ops.py", line 777, in random_uniform name=name) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 610, in _apply_op_helper param_name=input_name) File "/home/ying/anaconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 60, in _SatisfiesTypeConstraint ", ".join(dtypes.as_dtype(x).name for x in allowed_list))) TypeError: Value passed to parameter 'shape' has DataType float32 not in list of allowed values: int32, int64 ― You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADvEEBN6dmGZMGl-x0gncI73SEJ40TiQks5vcgVsgaJpZM4cVrbt> .

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#5 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AuiIIj96uE9xt4Rjt374rcZq000Mg4kAks5vciBjgaJpZM4cVrbt>.