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socket.gaierror: [Errno -2] Name or service not known at download-database ~/db

#176Openhandibles 创建于 2026-03-12
H
handiblescommented
Thanks for the great package. Getting the following conjoined errors in `download-database` with `v.1.11.2`: ``` socket.gaierror: [Errno -2] Name or service not known [...] urllib.error.URLError: <urlopen error [Errno -2] Name or service not known> ``` as per the errors below. Looks like a domain resolution issue - but not seeing any hints in `genomad/modules/download.py`... ``` mamba create -n gnmd -c conda-forge -c bioconda genomad -y conda activate gnmd genomad download-database ~/db # > Traceback (most recent call last): # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 1344, in do_open # > h.request(req.get_method(), req.selector, req.data, headers, # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1358, in request # > self._send_request(method, url, body, headers, encode_chunked) # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1404, in _send_request # > self.endheaders(body, encode_chunked=encode_chunked) # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1353, in endheaders # > self._send_output(message_body, encode_chunked=encode_chunked) # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1113, in _send_output # > self.send(msg) # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1057, in send # > self.connect() # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1492, in connect # > super().connect() # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/http/client.py", line 1023, in connect # > self.sock = self._create_connection( # > ^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/socket.py", line 841, in create_connection # > for res in getaddrinfo(host, port, 0, SOCK_STREAM): # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/socket.py", line 978, in getaddrinfo # > for res in _socket.getaddrinfo(host, port, family, type, proto, flags): # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > socket.gaierror: [Errno -2] Name or service not known # > # > During handling of the above exception, another exception occurred: # > # > Traceback (most recent call last): # > File "/home/user/bin/miniforge3/envs/gnmd/bin/genomad", line 10, in <module> # > sys.exit(cli()) # > ^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/rich_click/rich_command.py", line 402, in __call__ # > return super().__call__(*args, **kwargs) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/click/core.py", line 1485, in __call__ # > return self.main(*args, **kwargs) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/rich_click/rich_command.py", line 216, in main # > rv = self.invoke(ctx) # > ^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/click/core.py", line 1873, in invoke # > return _process_result(sub_ctx.command.invoke(sub_ctx)) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/click/core.py", line 1269, in invoke # > return ctx.invoke(self.callback, **ctx.params) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/click/core.py", line 824, in invoke # > return callback(*args, **kwargs) # > ^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/genomad/cli.py", line 355, in download_database # > genomad.download.main(destination, keep, verbose) # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/genomad/modules/download.py", line 85, in main # > database_downloader = DatabaseDownloader(destination, console) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/genomad/modules/download.py", line 24, in __init__ # > self.version = str(version) if version else self.get_version() # > ^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/site-packages/genomad/modules/download.py", line 32, in get_version # > urllib.request.urlopen(self.base_url + "releases.txt") # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 215, in urlopen # > return opener.open(url, data, timeout) # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 515, in open # > response = self._open(req, data) # > ^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 532, in _open # > result = self._call_chain(self.handle_open, protocol, protocol + # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 492, in _call_chain # > result = func(*args) # > ^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 1392, in https_open # > return self.do_open(http.client.HTTPSConnection, req, # > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ # > File "/home/user/bin/miniforge3/envs/gnmd/lib/python3.12/urllib/request.py", line 1347, in do_open # > raise URLError(err) ```
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