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hsgweon / pipits

Automated pipeline for analyses of fungal ITS from the Illumina
GNU General Public License v3.0
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[SSL: CERTIFICATE_VERIFY_FAILED] #54

Closed luongphekidz07 closed 1 year ago

luongphekidz07 commented 2 years ago

Hi,

I am running pipits in our cluster server with the command: "pipits_process -i /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_funits6/ITS.fasta -o /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6 -v -r"

However, I received the following errors: pipits_process -i /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_funits6/ITS.fasta -o /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6 -v -r pipits_process 2.8, the PIPITS Project https://github.com/hsgweon/pipits

2022-09-01 13:29:16 pipits_process started 2022-09-01 13:29:16 Generating a sample list from the input sequences 2022-09-01 13:29:35 Downloading UNITE trained database, version: 10.05.2021 Traceback (most recent call last): File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/connectionpool.py", line 600, in urlopen chunked=chunked) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/connectionpool.py", line 345, in _make_request self._validate_conn(conn) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/connectionpool.py", line 844, in _validate_conn conn.connect() File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/connection.py", line 326, in connect sslcontext=context) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/util/ssl.py", line 325, in ssl_wrap_socket return context.wrap_socket(sock, server_hostname=server_hostname) File "/home/nguyenl15/.conda/envs/pipits_env/lib/python3.6/ssl.py", line 407, in wrap_socket _context=self, _session=session) File "/home/nguyenl15/.conda/envs/pipits_env/lib/python3.6/ssl.py", line 817, in init self.do_handshake() File "/home/nguyenl15/.conda/envs/pipits_env/lib/python3.6/ssl.py", line 1077, in do_handshake self._sslobj.do_handshake() File "/home/nguyenl15/.conda/envs/pipits_env/lib/python3.6/ssl.py", line 689, in do_handshake self._sslobj.do_handshake() ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/adapters.py", line 438, in send timeout=timeout File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/packages/urllib3/connectionpool.py", line 630, in urlopen raise SSLError(e) requests.packages.urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/nguyenl15/.conda/envs/pipits_env/bin/pipits_process", line 344, in verbose = options.verbose) File "/home/nguyenl15/.conda/envs/pipits_env/bin/pipits_process", line 272, in downloadDB request = requests.get(url, stream=True) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/api.py", line 72, in get return request('get', url, params=params, kwargs) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/api.py", line 58, in request return session.request(method=method, url=url, kwargs) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/sessions.py", line 518, in request resp = self.send(prep, send_kwargs) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/sessions.py", line 661, in send history = [resp for resp in gen] if allow_redirects else [] File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/sessions.py", line 661, in history = [resp for resp in gen] if allow_redirects else [] File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/sessions.py", line 214, in resolve_redirects adapter_kwargs File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/sessions.py", line 639, in send r = adapter.send(request, **kwargs) File "/hpc/apps/anaconda/anaconda3/lib/python3.4/site-packages/requests/adapters.py", line 512, in send raise SSLError(e, request=request) requests.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)

Could you please suggest me the solution?

Thank you, Kind regards, Le Phuong Nguyen.