connect error of q2-clawback

[RayLin]

Hi everyone
I found an error in q2-clawback (it seems a connection error).
The command I ran were:
qiime clawback summarize-Qiita-metadata-category-and-contexts
–p-category empo_3
–o-visualization available_empo3.qzv

and the error message was:

Plugin error from clawback:

HTTPConnectionPool(host=‘qiita.ucsd.edu’, port=7329): Max retries exceeded with url: /HKEYS/metadata:category:empo_3 (Caused by NewConnectionError(’<urllib3.connection.HTTPConnection object at 0x7f7be56d0320>: Failed to establish a new connection: [Errno 110] Connection timed out’,))

Debug info has been saved to /tmp/qiime2-q2cli-err-tpnukf20.log

logfile:

tail -f /tmp/qiime2-q2cli-err-tpnukf20.log
File “/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/requests/sessions.py”, line 555, in get
return self.request(‘GET’, url, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/requests/sessions.py”, line 542, in request
resp = self.send(prep, **send_kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/requests/sessions.py”, line 655, in send
r = adapter.send(request, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2020.11/lib/python3.6/site-packages/requests/adapters.py”, line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host=‘qiita.ucsd.edu’, port=7329): Max retries exceeded with url: /HKEYS/metadata:category:empo_3 (Caused by NewConnectionError(’<urllib3.connection.HTTPConnection object at 0x7f7be56d0320>: Failed to establish a new connection: [Errno 110] Connection timed out’,))

If it’s a connection error, can I download the empo file from other site?

[Nicholas_Bokulich]

Hi @RayLin ,
This looks like an issue connecting to Qiita. I just checked the Qiita website and they are updating the system today... so I suspect that is the cause.

You could probably try again tomorrow (or whenever the system update is complete).

@RayLin

If it’s a connection error, can I download the empo file from other site?

Sure! clawback can take any taxonomy data as input. Check out the " Assembling More Exotic Weights" section of this tutorial. The first step uses redbiom to get a biom table of samples x ASVs, but this could be replaced by other sources, e.g., grabbing data from the Earth Microbiome Project or another source.

Using q2-clawback to assemble taxonomic weights

Note: This guide assumes you have installed QIIME 2 using one of the procedures in the install documents. This tutorial extends the q2-feature-classifier tutorial to show how you can improve taxonomic classification accuracy by assembling ecologically informed taxonomic weights for your samples using q2-clawback. This approach is described in this article: https://doi.org/10.1038/s41467-019-12669-6 We will retrain the naive Bayes classifier from the q2-feature-classifier to classify the ski…

Good luck!

[RayLin]

Thank you @Nicholas_Bokulich !
I will try to connect again these days, and also try to get ASVs from Earth Microbiome Project.

Best regards!

Ray

[RayLin]

I still can not connect to Qiita from Mar 15 until today. It reminds me that maybe in our institute, some of the connection ports were blocked by firewall. Than I tried to access internet via my iphone shared Wifi, and it works. Hope this information can help someone who also meet the same connection error.