model predictions in google collab

MMSplice version:
Python version: 3.7
Operating System: Google Collab

Description

Hi, I am trying to run the google collab notebook with the test vcf data and the notebook seems to crash once you try to make the predictions (so after the model is built). I run this command:

predict_save(model, dl, output_csv, pathogenicity=True, splicing_efficiency=True)

This is what the output looks like:

0it [00:00, ?it/s]

WARNING:tensorflow:Model was constructed with shape (None, None, 4) for input KerasTensor(type_spec=TensorSpec(shape=(None, None, 4), dtype=tf.float32, name='input_5'), name='input_5', description="created by layer 'input_5'"), but it was called on an input with incompatible shape (32,).

0it [00:00, ?it/s]

---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

<ipython-input-58-81048a45f553> in <module>()
----> 1 predict_save(model, dl, output_csv, pathogenicity=True, splicing_efficiency=True)

6 frames

/usr/local/lib/python3.7/dist-packages/tensorflow/python/framework/func_graph.py in autograph_handler(*args, **kwargs)
   1127           except Exception as e:  # pylint:disable=broad-except
   1128             if hasattr(e, "ag_error_metadata"):
-> 1129               raise e.ag_error_metadata.to_exception(e)
   1130             else:
   1131               raise

ValueError: in user code:

    File "/usr/local/lib/python3.7/dist-packages/keras/engine/training.py", line 1621, in predict_function  *
        return step_function(self, iterator)
    File "/usr/local/lib/python3.7/dist-packages/keras/engine/training.py", line 1611, in step_function  **
        outputs = model.distribute_strategy.run(run_step, args=(data,))
    File "/usr/local/lib/python3.7/dist-packages/keras/engine/training.py", line 1604, in run_step  **
        outputs = model.predict_step(data)
    File "/usr/local/lib/python3.7/dist-packages/keras/engine/training.py", line 1572, in predict_step
        return self(x, training=False)
    File "/usr/local/lib/python3.7/dist-packages/keras/utils/traceback_utils.py", line 67, in error_handler
        raise e.with_traceback(filtered_tb) from None
    File "/usr/local/lib/python3.7/dist-packages/keras/engine/input_spec.py", line 227, in assert_input_compatibility
        raise ValueError(f'Input {input_index} of layer "{layer_name}" '

    ValueError: Exception encountered when calling layer "model_5" (type Functional).

    Input 0 of layer "conv" is incompatible with the layer: expected min_ndim=3, found ndim=1. Full shape received: (32,)

    Call arguments received:
      • inputs=tf.Tensor(shape=(32,), dtype=string)
      • training=False
      • mask=None

gagneurlab / MMSplice_MTSplice

model predictions in google collab #56

Description