Comments (4)
@ranijames v0.5.6 of Nucleus requires TF 2.3.0. Could you try running the notebook with TF 2.3.0?
from nucleus.
@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
from nucleus.
@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).
from nucleus.
Closing this issue out, but feel free to reopen if you have any other questions @ranijames!
from nucleus.
Related Issues (20)
- Install process is completely broken in presence of existing tensorflow install, and breaks that also HOT 5
- User Menu for Nucleus HOT 2
- hdf5 file format not supported HOT 3
- Is there any limitation for calling rare mutation? HOT 2
- MD tag HOT 2
- ImportError for `nucleus.io.gfile` HOT 2
- RuntimeError: PythonNext() argument variant is not valid: Dynamic cast failed. HOT 1
- Nucleus Proto is colliding with Tensorflow protos? HOT 8
- Failed to install google-nucleus HOT 2
- Nucleus Proto is colliding with Tensorflow protos HOT 7
- Error runing codelab : dna_sequencing_error_correction HOT 4
- Read strand HOT 1
- ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory HOT 3
- Nucleus not building for Python3.7-3.9 via pip. HOT 5
- Compatibility with Tensorflow 2.11.0 HOT 2
- install google-nucleus error HOT 14
- PythonNext() argument read is not valid HOT 2
- PythonNext() argument read is not valid: Dynamic cast failed
- Complex version of error correction example?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from nucleus.