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Colab notebook enformer-training.ipynb does not iterate properly

Open majanoack opened this issue 1 year ago • 0 comments

When I run the provided notebook "enformer-training.ipynb" on colab I run into the following error when I include the basenji_barnyard-dataset as stated here #367:

OutOfRangeError Traceback (most recent call last) /usr/local/lib/python3.10/dist-packages/tensorflow/python/data/ops/iterator_ops.py in next(self) 796 try: --> 797 return self._next_internal() 798 except errors.OutOfRangeError:

4 frames /usr/local/lib/python3.10/dist-packages/tensorflow/python/data/ops/iterator_ops.py in _next_internal(self) 779 with context.execution_mode(context.SYNC): --> 780 ret = gen_dataset_ops.iterator_get_next( 781 self._iterator_resource,

/usr/local/lib/python3.10/dist-packages/tensorflow/python/ops/gen_dataset_ops.py in iterator_get_next(iterator, output_types, output_shapes, name) 3015 except _core._NotOkStatusException as e: -> 3016 _ops.raise_from_not_ok_status(e, name) 3017 except _core._FallbackException:

/usr/local/lib/python3.10/dist-packages/tensorflow/python/framework/ops.py in raise_from_not_ok_status(e, name) 7261 e.message += (" name: " + name if name is not None else "") -> 7262 raise core._status_to_exception(e) from None # pylint: disable=protected-access 7263

OutOfRangeError: {{function_node _wrapped__IteratorGetNext_output_types_2_device/job:localhost/replica:0/task:0/device:CPU:0}} End of sequence [Op:IteratorGetNext]

During handling of the above exception, another exception occurred:

StopIteration Traceback (most recent call last) in <cell line: 2>() 1 it = iter(mouse_dataset) ----> 2 example = next(it)

/usr/local/lib/python3.10/dist-packages/tensorflow/python/data/ops/iterator_ops.py in next(self) 797 return self._next_internal() 798 except errors.OutOfRangeError: --> 799 raise StopIteration 800 801 @property

StopIteration:

Is this a tensorflow version issue or is the dataset I am using not the correct one? Please help!

majanoack avatar Jul 31 '23 16:07 majanoack