Installed Greengenes2 and redbiom in Qiime2 but getting a connection error

[waalkes]

I am trying to get Greengenes2 and redbiom working in Qiime2. I am using this tutorial:

https://forum.qiime2.org/t/querying-for-public-microbiome-data-in-qiita-using-redbiom/4653

but when I try the first command: redbiom summarize contexts

I get the error below. I see that at times there have been server issues. Any help getting me going?

Thanks,

Adam +++++++++++++++++++++++++++++++++++ Traceback (most recent call last): File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connection.py", line 203, in _new_conn sock = connection.create_connection( File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out

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

Traceback (most recent call last): File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connectionpool.py", line 791, in urlopen response = self._make_request( File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connectionpool.py", line 497, in _make_request conn.request( File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connection.py", line 395, in request self.endheaders() File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/http/client.py", line 1251, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/http/client.py", line 1011, in _send_output self.send(msg) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/http/client.py", line 951, in send self.connect() File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connection.py", line 243, in connect self.sock = self._new_conn() File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connection.py", line 218, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7f3e92eee160>: Failed to establish a new connection: [Errno 110] Connection timed out

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

Traceback (most recent call last): File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/requests/adapters.py", line 486, in send resp = conn.urlopen( File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/connectionpool.py", line 845, in urlopen retries = retries.increment( File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/urllib3/util/retry.py", line 515, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='qiita.ucsd.edu', port=7329): Max retries exceeded with url: /HGETALL/state:contexts.json (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f3e92eee160>: Failed to establish a new connection: [Errno 110] Connection timed out'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/bin/redbiom", line 8, in sys.exit(cli()) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/redbiom/commands/summarize.py", line 16, in summarize_caches contexts = redbiom.summarize.contexts() File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/redbiom/summarize.py", line 29, in contexts contexts = get('state', 'HGETALL', 'contexts') File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/redbiom/_requests.py", line 95, in f return _parse_validate_request(s.get(url), cmd) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/requests/sessions.py", line 602, in get return self.request("GET", url, kwargs) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, send_kwargs) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, kwargs) File "/mnt/home/waalkes/miniconda3/envs/qiime2-amplicon-2023.9/lib/python3.8/site-packages/requests/adapters.py", line 519, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPConnectionPool(host='qiita.ucsd.edu', port=7329): Max retries exceeded with url: /HGETALL/state:contexts.json (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f3e92eee160>: Failed to establish a new connection: [Errno 110] Connection timed out'))

[wasade]

Hi @waalkes, thanks for reaching out! This would happen your system is unable to connect with qiita.ucsd.edu on port 7329. It can happen sporadically. I cannot recreate it right now, and don't have an indication of services being down. Would it be possible to retry the redbiom summarize contexts call?

[waalkes]

Thanks for the quick response. I can ping the site just fine but I still get the error. Let me check with our guys about the port or if there is anything that might be an issue on our side.

[waalkes]

It was a firewall issue. Opened the port and it is working. Thanks!

[wasade]

Wonderful, glad to hear!!