Can you recommend a redbiom context for clawback?

Community Plugin Support
1

Hello,

I am trying to produce a classifier specific to the soil (non-saline) environment as well as being specific for the V3V4 primers utilised by Eurofins (357f - 800r). I utilised this tutorial and SILVA 138.1 to produce a primer specific classifier and now I would like to use clawback to retrain my classifier to the soil specific environment. I am wondering what I need to include under ( --p-context) to achieve this?

qiime clawback assemble-weights-from-Qiita
--i-classifier silva-138.1-ssu-nr99-357f-800r-classifier.qza \
--i-reference-taxonomy silva-138.1-ssu-nr99-tax-357f-800r-derep-uniq.qza
--i-reference-sequences silva-138.1-ssu-nr99-seqs-357f-800r-uniq.qza
--p-metadata-key empo_3
--p-metadata-value "Soil (non‑saline)" \
--p-context ??????
--o-class-weight my-138-1-weights.qza
--p-n-jobs 2

I have tried running:

qiime clawback summarize-Qiita-metadata-category-and-contexts
--p-category empo_3
--o-visualization available_empo3.qzv

to see what the available contexts are... however I got this error message:

Plugin error from clawback:

HTTPConnectionPool(host='qiita.ucsd.edu', port=7329): Max retries exceeded with url: /HKEYS/metadata:category:empo_3.json (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fdc845ad670>: Failed to establish a new connection: [Errno 60] Operation timed out'))

Unsure where to go from here.

Thanks in advance of your response!

All the best,
Callum

7

Hey @Cal ,
It looks like the issue is with your system; it is unable to reach outside networks or is firewalling ports.

You can see this topic for a similar error message (though in that case the issue was on the server side, in this case it looks like a firewall issue on your end):

You could try running redbiom directly (per that topic) to get a full error log to use for debugging, and discuss with your system admin to see if they can identify the connection issue.

Good luck!

2 Likes
9

Hi @Cal and @Nicholas_Bokulich,

It looks like Cal is having some network issues, but the original question is valid, because Qiita contexts are a moving target.

For anyone coming to this later, the best Qiita context to use with clawback is currently Deblur_2021.09-Illumina-16S-V4-150nt-ac8c0b (as of early 2022).

This will change in future, so please use

qiime clawback summarize-Qiita-metadata-category-and-contexts \
    --p-category empo_3 \
    --o-visualization result-to-view-using-qiime-tools-view.qzv

to find the best context to use. The one you want is the one with the most samples that has Deblur and 150nt somewhere in its cryptic-to-the-uninitiated name.

Ben