ValueError: Connection error, and we cannot find the requested files in the cached path. Please try again or make sure your Internet connection is on.

[ly-318]

When trying to run the test i always get this error.

(base) emma@emma-X570S-AORUS-MASTER:/media/emma/HD1/LY/viral-protein-function-plm$ conda activate plm_vpf_embed
(plm_vpf_embed) emma@emma-X570S-AORUS-MASTER:/media/emma/HD1/LY/viral-protein-function-plm$ python scripts/embed_faa.py -faa test/test.faa -out test_out
Traceback (most recent call last):
File "scripts/embed_faa.py", line 37, in
main()
File "scripts/embed_faa.py", line 33, in main
embedding = protbert_bfd_embed(faa_path=faa_path, max_length=MAX_LENGTH, num_gpus=NUM_GPU, batch_size=BATCH_SIZE)
File "/media/emma/HD1/LY/viral-protein-function-plm/scripts/protbert_bfd_embed_utils.py", line 42, in protbert_bfd_embed
transformer_bfd = BioTransformers(backend='protbert_bfd', num_gpus=num_gpus)
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/utils/deprecated.py", line 10, in wrapper
return f(*args, **kwargs)
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/utils/deprecated.py", line 10, in wrapper
return f(*args, **kwargs)
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/bio_transformers.py", line 55, in new
num_gpus=num_gpus,
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/wrappers/transformers_wrappers.py", line 64, in init
model_dir=model_dir, device=device
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/wrappers/rostlab_wrapper.py", line 39, in init
model_dir, do_lower_case=False, padding=True
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/tokenization_utils_base.py", line 1680, in from_pretrained
user_agent=user_agent,
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/file_utils.py", line 1337, in cached_path
local_files_only=local_files_only,
File "/home/emma/miniforge3/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/file_utils.py", line 1553, in get_from_cache
"Connection error, and we cannot find the requested files in the cached path."
ValueError: Connection error, and we cannot find the requested files in the cached path. Please try again or make sure your Internet connection is on.
(plm_vpf_embed) emma@emma-X570S-AORUS-MASTER:/media/emma/HD1/LY/viral-protein-function-plm$

[ly-318]

I got errors when i try to run this python script to download the model：
from transformers import BertForMaskedLM, BertTokenizer
BertTokenizer.from_pretrained('/media/emma/HD1/LY/prot_bert_bfd', do_lower_case=False, padding=True)
BertForMaskedLM.from_pretrained('/media/emma/HD1/LY/prot_bert_bfd')

Some weights of the model checkpoint at /media/emma/HD1/LY/prot_bert_bfd were not used when initializing BertForMaskedLM: ['cls.seq_relationship.bias', 'cls.seq_relationship.weight']

• This IS expected if you are initializing BertForMaskedLM from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).
• This IS NOT expected if you are initializing BertForMaskedLM from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).

[zachflam]

Hi, thank you for reaching out. I have had others encounter this error before. Are you attempting to run the model on a cluster node?

[syunwun]

Hi! I think I also met the same problem on both Colab and HPC.
Here is the error message when I run the test file on Colab in this part, "4. Embed proteins using protein language model".

---

File "scripts/embed_faa.py", line 37, in
main()
File "scripts/embed_faa.py", line 33, in main
embedding = protbert_bfd_embed(faa_path=faa_path, max_length=MAX_LENGTH, num_gpus=NUM_GPU, batch_size=BATCH_SIZE)
File "/content/viral-protein-function-plm/scripts/protbert_bfd_embed_utils.py", line 42, in protbert_bfd_embed
transformer_bfd = BioTransformers(backend='protbert_bfd', num_gpus=num_gpus)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/utils/deprecated.py", line 10, in wrapper
return f(*args, **kwargs)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/utils/deprecated.py", line 10, in wrapper
return f(*args, **kwargs)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/bio_transformers.py", line 55, in new
num_gpus=num_gpus,
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/wrappers/transformers_wrappers.py", line 64, in init
model_dir=model_dir, device=device
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/biotransformers/wrappers/rostlab_wrapper.py", line 39, in init
model_dir, do_lower_case=False, padding=True
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/tokenization_utils_base.py", line 1680, in from_pretrained
user_agent=user_agent,
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/file_utils.py", line 1337, in cached_path
local_files_only=local_files_only,
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/file_utils.py", line 1592, in get_from_cache
http_get(url_to_download, temp_file, proxies=proxies, resume_size=resume_size, headers=headers)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/transformers/file_utils.py", line 1439, in http_get
r = requests.get(url, stream=True, proxies=proxies, headers=headers)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/sessions.py", line 498, in prepare_request
hooks=merge_hooks(request.hooks, self.hooks),
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/models.py", line 368, in prepare
self.prepare_url(url, params)
File "/opt/conda/envs/plm_vpf_embed/lib/python3.7/site-packages/requests/models.py", line 440, in prepare_url
f"Invalid URL {url!r}: No scheme supplied. "
requests.exceptions.MissingSchema: Invalid URL '/api/resolve-cache/models/Rostlab/prot_bert_bfd/6c5c8a55a52ff08a664dfd584aa1773f125a0487/vocab.txt?%2FRostlab%2Fprot_bert_bfd%2Fresolve%2Fmain%2Fvocab.txt=&etag=%226fc4cfbdaf88194e894ef1ab9c394f3d5171e596%22': No scheme supplied. Perhaps you meant https:///api/resolve-cache/models/Rostlab/prot_bert_bfd/6c5c8a55a52ff08a664dfd584aa1773f125a0487/vocab.txt?%2FRostlab%2Fprot_bert_bfd%2Fresolve%2Fmain%2Fvocab.txt=&etag=%226fc4cfbdaf88194e894ef1ab9c394f3d5171e596%22?

[zachflam]

I am sorry for taking so long to get back to this. v2, which we just released, no longer relies on an old dependency which was the cause of this issue. You can try downloading the repo again and reinstalling.