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gunjanbaid avatar gunjanbaid commented on July 28, 2024

@ranijames v0.5.6 of Nucleus requires TF 2.3.0. Could you try running the notebook with TF 2.3.0?

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ranijames avatar ranijames commented on July 28, 2024

@gunjanbaid Thanks for the reply. I have created a new environment with TF 2.3.0. And tried to run the code in the notebook. Now, when I try to import all the modules it is throwing a new error,

TypeError                                 Traceback (most recent call last)
<ipython-input-3-36045406c016> in <module>
      8 import numpy as np
      9 
---> 10 from nucleus.io import fasta
     11 from nucleus.io import sam
     12 from nucleus.io import vcf

~/anaconda3/envs/nucleus/lib/python3.8/site-packages/nucleus/io/fasta.py in <module>
     45 from nucleus.io import genomics_reader
     46 from nucleus.io.python import reference
---> 47 from nucleus.protos import fasta_pb2
     48 from nucleus.protos import reference_pb2
     49 from nucleus.util import ranges

~/anaconda3/envs/nucleus/lib/python3.8/site-packages/nucleus/protos/fasta_pb2.py in <module>
     14 
     15 
---> 16 from nucleus.protos import range_pb2 as nucleus_dot_protos_dot_range__pb2
     17 from nucleus.protos import reference_pb2 as nucleus_dot_protos_dot_reference__pb2
     18 

~/anaconda3/envs/nucleus/lib/python3.8/site-packages/nucleus/protos/range_pb2.py in <module>
     34   containing_type=None,
     35   fields=[
---> 36     _descriptor.FieldDescriptor(
     37       name='reference_name', full_name='nucleus.genomics.v1.Range.reference_name', index=0,
     38       number=1, type=9, cpp_type=9, label=1,

~/anaconda3/envs/nucleus/lib/python3.8/site-packages/google/protobuf/descriptor.py in __new__(cls, name, full_name, index, number, type, cpp_type, label, default_value, message_type, enum_type, containing_type, is_extension, extension_scope, options, serialized_options, has_default_value, containing_oneof, json_name, file)
    528                 has_default_value=True, containing_oneof=None, json_name=None,
    529                 file=None):  # pylint: disable=redefined-builtin
--> 530       _message.Message._CheckCalledFromGeneratedFile()
    531       if is_extension:
    532         return _message.default_pool.FindExtensionByName(full_name)

TypeError: Descriptors should not be created directly, but only retrieved from their parent.

Looking forward to your answer! Thanks

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gunjanbaid avatar gunjanbaid commented on July 28, 2024

@ranijames We have seen this issue caused by having an incompatible protobuf version. In addition to having Nucleus at 0.5.6 and TF at 2.3.0, you should not install protobuf directly beforehand (or if you do, pin it to 3.9.2).

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gunjanbaid avatar gunjanbaid commented on July 28, 2024

Closing this issue out, but feel free to reopen if you have any other questions @ranijames!

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