Comments (11)
kishorejaganathan
commented on August 14, 2024
When I googled your error, a lot of the links are pointing to Tensorflow 2.0. Could you open an interactive python session and just try:
import tensorflow as tf
print(tf.__version__)
and make sure you've installed the right version of Tensorflow (we've tested from 1.2 to 1.9)?
Some other things you could try:
- Install tensorflow via pip
- Try python 2.7 if that's an option
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kishorejaganathan
commented on August 14, 2024
Could you also try installing tensorflow via
conda install tensorflow==1.9.0
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davemcg
commented on August 14, 2024
I also saw that which is why I installed tensorflow at 1.2
(spliceai) [mcgaugheyd@cn4177 2019_arno]$ conda list tensorflow
# packages in environment at /data/mcgaugheyd/conda/envs/spliceai:
#
# Name Version Build Channel
tensorflow 1.2.0 py36_0 conda-forge
Though when I check via python....
>>> import tensorflow as tf
>>> print(tf.__version__)
2.0.0
Uh, what happened?
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kishorejaganathan
commented on August 14, 2024
Yeah I figured you installed 2.0 by mistake, usually it should be == and not = for precise versions. Could you try one of:
conda install tensorflow==1.9.0
or
pip install tensorflow==1.9.0
though I am not sure it will help as your conda list output is as expected...
During the next update, I'll add a patch to make sure it works for versions 2.0 onwards as well...
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davemcg
commented on August 14, 2024
Installed conda create --yes --name spliceai; conda activate spliceai; conda install --yes tensorflow==1.9-0; conda install --yes spliceai but now getting this error:
$ spliceai -h
Using TensorFlow backend.
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:523: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:524: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:527: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:532: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
File "/data/mcgaugheyd/conda/envs/spliceai/bin/spliceai", line 8, in <module>
from spliceai.__main__ import main
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/spliceai/__main__.py", line 4, in <module>
from spliceai.utils import Annotator, get_delta_scores
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/spliceai/utils.py", line 5, in <module>
from keras.models import load_model
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
from . import utils
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
from . import conv_utils
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
from .. import backend as K
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/backend/__init__.py", line 1, in <module>
from .load_backend import epsilon
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/backend/load_backend.py", line 90, in <module>
from .tensorflow_backend import *
File "/data/mcgaugheyd/conda/envs/spliceai/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 54, in <module>
get_graph = tf_keras_backend.get_graph
AttributeError: module 'tensorflow.python.keras.backend' has no attribute 'get_graph'
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kishorejaganathan
commented on August 14, 2024
Also seems like a 2.0 issue. Could you try installing tensorflow with pip?
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kishorejaganathan
commented on August 14, 2024
Is this still an issue? I'm reading that it is important to use certain versions of Keras with certain versions of Tensorflow. Could you try Keras==2.2.4 with Tensorflow 1.9 if you still couldn't get this to work?
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mcortes-lopez
commented on August 14, 2024
I had a similar issue and I tried the installation with Keras 2.24 and Tensorflow 1.9 but the error that i currently have is:
Traceback (most recent call last):
File "/home/mcortesl/.conda/envs/spliceai/bin/spliceai", line 12, in
sys.exit(main())
File "/home/mcortesl/.conda/envs/spliceai/lib/python3.6/site-packages/spliceai/main.py", line 53, in main
ann = Annotator(args.R, args.A)
File "/home/mcortesl/.conda/envs/spliceai/lib/python3.6/site-packages/spliceai/utils.py", line 20, in init
self.genes = df['#NAME'].get_values()
File "/home/mcortesl/.conda/envs/spliceai/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'Series' object has no attribute 'get_values'
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JakeHagen
commented on August 14, 2024
@mcortes-lopez I think that is a pandas 1.0 issue. Try pandas 0.25.3
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kishorejaganathan
commented on August 14, 2024
@mcortes-lopez: As pointed out by @JakeHagen, this is a pandas 1.0 issue. We have resolved this in the latest update to the git repo, so you should not have this issue if you clone it now. Alternately, you can also try downgrading pandas version to something like 0.24.2 and that should work as well...
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bw2
commented on August 14, 2024
Looks like tensorflow v1.9.0 is no longer available on PyPI
This works instead:
python3 -m pip install tensorflow==1.15.3
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