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jiujiezz / deephlapan

A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC
GNU General Public License v2.0
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Error in loading the saved optimizer state #9

Open songofbin opened 5 years ago

songofbin commented 5 years ago

Help: please tell me how to solve this problem, thanks!

$ /path/Anaconda2/bin/deephlapan -P LNIMNKLNI -H HLA-A02:01 Using TensorFlow backend.

    =====================================================================
    DeepHLApan is a deep learning approach used for predicting high-confidence 
    neoantigens by considering both the presentation possibilities of 
    mutant peptides and the potential immunogenicity of pMHC.

    Usage:

    Single peptide and HLA:

        deephlapan -P LNIMNKLNI -H HLA-A02:01 

    List of peptides and HLA alleles in a file:

        deephlapan -F [file] -O [output directory]  

        (see 1.csv in demo/ for the detailed format of input file)
    =====================================================================

2019-06-06 10:31:48.171028 Prediction starting.....

WARNING:tensorflow:From /path/Anaconda2/lib/python2.7/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. WARNING:tensorflow:From /path/Anaconda2/lib/python2.7/site-packages/Keras-2.2.4-py2.7.egg/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. 2019-06-06 10:31:52.526305: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399935000 Hz 2019-06-06 10:31:52.535517: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x55c0337b5540 executing computations on platform Host. Devices: 2019-06-06 10:31:52.535933: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , WARNING:tensorflow:From /path/Anaconda2/lib/python2.7/site-packages/tensorflow/python/ops/math_ops.py:3066: to_int32 (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. /path/Anaconda2/lib/python2.7/site-packages/Keras-2.2.4-py2.7.egg/keras/engine/saving.py:327: UserWarning: Error in loading the saved optimizer state. As a result, your model is starting with a freshly initialized optimizer. warnings.warn('Error in loading the saved optimizer ' 2019-06-06 10:36:54.549616 Prediction end

wujingcheng commented 5 years ago

This problem may be caused by the different version of Keras which is 2.0.8 in our training step. You can try to install the same version or use deephlapan by docker.

songofbin commented 5 years ago

Thanks!