clawback --metadata-value upper-/lowercase

arwqiime · February 3, 2022, 12:21pm

Hello,
A recent summary of 'q2 clawback summarize_Qiita_metadata_category_and_contexts' of the empo_3 categories showed that there are two entries for 'animal proximal gut', differing in the uppercase and lowercase letters for 'Animal/animal'. (see qzv)

Will this influence the weights created by 'assemble-weights-from-Qiita'?
Is it possible to use more than one metadata-value in clawback?

Best regards
available_empo3.qzv (185.7 KB)

Nicholas_Bokulich · February 3, 2022, 6:41pm

Hi @arwqiime ,

Check out the readytowear repo to see some usage examples. You can use multiple queries to capture both upper and lowercase (or better yet, different metadata values that you want to lump together, e.g., maybe you want to compile weights from all host-associated sample types?). See this example:

github.com

BenKaehler/readytowear/blob/master/scripts/assemble-weights.silva_138.sh#L27-L32


      
          qiime clawback fetch-Qiita-samples \
            --p-context Deblur-Illumina-16S-V4-150nt-780653 \
            --p-metadata-key empo_3 \
            --p-metadata-value 'Animal distal gut' \
            --p-metadata-value 'animal distal gut' \
            --o-samples $tmp/animal-distal-gut.qza &

arwqiime · February 4, 2022, 11:00am

Hi @Nicholas_Bokulich
Thank you for directing me to the reatytowear repo, I should have known to look there...

I get the following error with the command below:
"Can only support two comparisons"
I tried to combine the values in behind a single --p-metadata-value, spearated by commas, but it does not seem to be allowed here.

Any suggestion how to greate weights from animal gut samples?
Best,

qiime clawback assemble-weights-from-Qiita
--i-classifier silva-138.1-ssu-nr99-515f-806r-classifier.qza
--i-reference-sequences silva-138.1-ssu-nr99-seqs-515f-806r-derep-uniq.qza
--i-reference-taxonomy silva-138.1-ssu-nr99-tax-515f-806r-derep-uniq.qza
--p-metadata-key empo_3
--p-metadata-value 'Animal distal gut'
--p-metadata-value 'animal distal gut'
--p-metadata-value 'animal proximal gut'
--p-metadata-value 'Animal proximal gut'
--p-metadata-value 'Animal-distal-gut'
--p-context Deblur_2021.09-Illumina-18S-V4-150nt-ac8c0b
--o-class-weight silva-138.1-ssu-nr99-515f-806r-weight_Animal-gut.qza
--p-reads-per-batch 'auto'
--p-n-jobs 40

Nicholas_Bokulich · February 4, 2022, 11:27am

can you please share the full error message?

arwqiime · February 4, 2022, 11:43am

Yes, of course!
The zip file contains the error message for two commands with multiple --p-metadata-values and with comma-separated values.
clawback-errors.zip (1.5 KB)

BenKaehler · February 4, 2022, 12:50pm

Hi @arwqiime, thanks @Nicholas_Bokulich,

Please just use one metadata value of “Animal distal gut”. It will give you an order of magnitude more data than you need.

I will debug your usage over the next day or so (I think I see the problem but I can’t confirm right now), but even after I fix it I would just advise using “Animal distal gut” only.

arwqiime · February 4, 2022, 1:44pm

Hi @BenKaehler
Thank you for your advice!
Best,

arwqiime · February 7, 2022, 1:33pm

Hi @BenKaehler ,
I realized a typo in my command shown above. The context should be '16S'...
Sorry, the last 6 digits were identical to the 18S one, and I overlooked this.

system · March 10, 2022, 7:33pm

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