DeepSEA test error
See original GitHub issueHi! I’m trying to run the DeepSEA predict example, but I am running into the following error:
(py36) [arun@login3 project-sriram]$ python
Python 3.6.5 | packaged by conda-forge | (default, Apr 6 2018, 13:39:56)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import kipoi
>>> model = kipoi.get_model('DeepSEA/predict')
Already up-to-date.
>>> pred = model.pipeline.predict_example()
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/pipeline.py", line 84, in predict_example
pred_list.append(self.model.predict_on_batch(batch['inputs']))
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/model.py", line 757, in predict_on_batch
pred, _ = self.np_run_pred(x)
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/model.py", line 788, in np_run_pred
pred = self.model(input)
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 206, in __call__
result = self.forward(*input, **kwargs)
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/container.py", line 64, in forward
input = module(input)
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/nn/modules/module.py", line 206, in __call__
result = self.forward(*input, **kwargs)
File "model_files/deepsea_cpu.py", line 89, in forward
File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/torch/autograd/variable.py", line 63, in __getattr__
raise AttributeError(name)
AttributeError: shape
This is from running the example code here: http://kipoi.org/models/DeepSEA/predict/
I installed kipoi using pip, as well as the dependencies pybedtools, pyfaidx. I installed pytorch using conda.
Any ideas here?
Issue Analytics
- State:
- Created 5 years ago
- Comments:5 (3 by maintainers)
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Hmm weird. That command results in:
I will try and update pytorch myself and see if that helps.
If you keep having this problem, try updating / upgrading conda itself by
conda update conda
and then try to usekipoi env create DeepSEA/predict
. also keep in mind that this command has to be run outside of environments. A similar issue with pytorch had been reported here: https://discuss.pytorch.org/t/issues-installing-pytorch-for-os-x-with-conda/11496/9 hope this helps