DeepSEA test error

Hi! 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?

[arundurvasula]

Hmm weird. That command results in:

(py36) [arun@login3 project-sriram]$ kipoi env create DeepSEA/predict
INFO [kipoi.cli.env] Writing environment file: /tmp/kipoi/envfiles/2c223561
INFO [kipoi.cli.env] Loading model: DeepSEA/predict description
INFO [kipoi.remote] Update /u/home/a/arun/.kipoi/models/
Already up-to-date.
INFO [kipoi.cli.env] Inferred dataloader name: DeepSEA/predict from the model.
INFO [kipoi.cli.env] Environment name: kipoi-DeepSEA__predict
INFO [kipoi.cli.env] Output env file: /tmp/kipoi/envfiles/2c223561/kipoi-DeepSEA                                                __predict.yaml
INFO [kipoi.cli.env] Done writing the environment file!
INFO [kipoi.cli.env] Creating conda env from file: /tmp/kipoi/envfiles/2c223561/                                                kipoi-DeepSEA__predict.yaml
Using Anaconda API: https://api.anaconda.org
Fetching package metadata ...............
Solving package specifications: .


NoPackagesFoundError: Dependency missing in current linux-64 channels:
  - pytorch-cpu >=0.2.0 -> mkl >=2018


Traceback (most recent call last):
  File "/u/home/a/arun/anaconda3/envs/py36/bin/kipoi", line 11, in <module>
    sys.exit(main())
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/__m                                                ain__.py", line 74, in main
    command_fn(args.command, sys.argv[2:])
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/cli                                                /env.py", line 307, in cli_main
    command_fn(args.command, raw_args[1:])
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/cli                                                /env.py", line 231, in cli_create
    kipoi.conda.create_env_from_file(env_file)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 78, in create_env_from_file
    return _call_conda(cmd_list, use_stdout=True)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 162, in _call_conda
    return _call_command("conda", extra_args, use_stdout)
  File "/u/home/a/arun/anaconda3/envs/py36/lib/python3.6/site-packages/kipoi/con                                                da.py", line 149, in _call_command
    raise subprocess.CalledProcessError(return_code, cmd_list)
subprocess.CalledProcessError: Command '['conda', 'env', 'create', '--file', '/t                                                mp/kipoi/envfiles/2c223561/kipoi-DeepSEA__predict.yaml']' returned non-zero exit                                                 status 1.

I will try and update pytorch myself and see if that helps.

[krrome]

If you keep having this problem, try updating / upgrading conda itself by conda update conda and then try to use kipoi 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