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sacdallago / bio_embeddings

Get protein embeddings from protein sequences
http://docs.bioembeddings.com
MIT License
468 stars 66 forks source link

Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host> #223

Open Azai-yx opened 1 year ago

Azai-yx commented 1 year ago

Metadata

key value
version 0.2.2
cuda True

Parameter

key value
type embed
protocol prottrans_t5_xl_u50
half_precision_model True
half_precision True
simple_remapping True

Traceback

Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 1354, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 1256, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 1302, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 1251, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 1011, in _send_output
    self.send(msg)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 951, in send
    self.connect()
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/http/client.py", line 922, in connect
    self.sock = self._create_connection(
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/socket.py", line 808, in create_connection
    raise err
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/socket.py", line 796, in create_connection
    sock.connect(sa)
OSError: [Errno 113] No route to host

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/site-packages/bio_embeddings/utilities/pipeline.py", line 284, in execute_pipeline_from_config
    stage_output_parameters = stage_runnable(**stage_parameters)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/site-packages/bio_embeddings/embed/pipeline.py", line 400, in run
    embedder: EmbedderInterface = embedder_class(**result_kwargs)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/site-packages/bio_embeddings/embed/prottrans_t5_embedder.py", line 55, in __init__
    super().__init__(**kwargs)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/site-packages/bio_embeddings/embed/embedder_interfaces.py", line 59, in __init__
    self._options[directory] = get_model_directories_from_zip(
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/site-packages/bio_embeddings/utilities/remote_file_retriever.py", line 78, in get_model_directories_from_zip
    with request.urlopen(req) as response, open(file_name, 'wb') as outfile:
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 525, in open
    response = self._open(req, data)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 542, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 502, in _call_chain
    result = func(*args)
  File "/home/ubuntu/anaconda3/envs/bio_emb/lib/python3.8/urllib/request.py", line 1383, in http_open
    return self.do_open(http.client.HTTPConnection, req)
urllib.error.URLError: <urlopen error [Errno 113] No route to host>

More info

Azai-yx commented 1 year ago

hello there. I recently need to embed 13-aa-long peptides to do a regression task. I am trying use light attention example config, and got this error reported. A further concern is that I am confused if this pretrain model is suitable for embed peptides instead of a long protein sequences. Theoratically, I assume peptides could also be embedded right?