phold run error

[ChaoXianSen]

• phold version: version 0.2.0
• Python version: Python 3.11.9
• Operating System: Linux sil1c4u26-admin7 3.10.0-957.el7.x86_64

Description

phold run -i ./pharokka_output/pharokka.gbk -o phold_output -t 8

I am trying to run phold on the output of pharokka, I get the following error:

Traceback (most recent call last):
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connectionpool.py", line 466, in _make_request
self._validate_conn(conn)
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connectionpool.py", line 1095, in _validate_conn
conn.connect()
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connection.py", line 652, in connect
sock_and_verified = _ssl_wrap_socket_and_match_hostname(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connection.py", line 805, in ssl_wrap_socket_and_match_hostname
ssl_sock = ssl_wrap_socket(
^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/util/ssl.py", line 465, in ssl_wrap_socket
ssl_sock = ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/util/ssl.py", line 509, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/ssl.py", line 1104, in _create
self.do_handshake()
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/ssl.py", line 1382, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1006)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connectionpool.py", line 789, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connectionpool.py", line 490, in _make_request
raise new_e
urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1006)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/requests/adapters.py", line 667, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/connectionpool.py", line 843, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/urllib3/util/retry.py", line 519, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /Rostlab/ProstT5_fp16/resolve/main/tokenizer_config.json (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1006)')))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/bin/phold", line 10, in
sys.exit(main())
^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/phold/init.py", line 1382, in main
main_cli()
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/phold/init.py", line 293, in run
subcommand_predict(
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/phold/subcommands/predict.py", line 161, in subcommand_predict
prediction_success = get_embeddings(
^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/phold/features/predict_3Di.py", line 433, in get_embeddings
model, vocab = get_T5_model(model_dir, model_name, cpu)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/phold/features/predict_3Di.py", line 160, in get_T5_model
vocab = T5Tokenizer.from_pretrained(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/transformers/tokenization_utils_base.py", line 2029, in from_pretrained
resolved_config_file = cached_file(
^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/transformers/utils/hub.py", line 399, in cached_file
resolved_file = hf_hub_download(
^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 1221, in hf_hub_download
return _hf_hub_download_to_cache_dir(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 1282, in _hf_hub_download_to_cache_dir
(url_to_download, etag, commit_hash, expected_size, head_call_error) = _get_metadata_or_catch_error(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 1722, in _get_metadata_or_catch_error
metadata = get_hf_file_metadata(url=url, proxies=proxies, timeout=etag_timeout, headers=headers)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 1645, in get_hf_file_metadata
r = _request_wrapper(
^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 372, in _request_wrapper
response = _request_wrapper(
^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/file_download.py", line 395, in _request_wrapper
response = get_session().request(method=method, url=url, **params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/huggingface_hub/utils/_http.py", line 66, in send
return super().send(request, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/pholdENV/lib/python3.11/site-packages/requests/adapters.py", line 698, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: (MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /Rostlab/ProstT5_fp16/resolve/main/tokenizer_config.json(Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1006)')))"), '(Request ID: bbcb5bf5-4179-4e8a-865b-176873fdf84c)')

Where is is an error in the run?

Looking forward to your reply!

[gbouras13]

Hi @ChaoXianSen ,

This is probably a hugging face blocked in China (looks like you are in China from your account!) issue.

Pholddb should be installable without hugging face thanks to the mirror for ProstT5 I uploaded on zenodo.

Try adding TRANSFORMERS_OFFLINE=True before running phold.

George