Plugin error from q2-longitudinal

[Diki (Diki P)]

Hi everyone,

I am running a longitudinal analysis with q2-longitudinal and an error occurred.
Below is the complete error message:

Plugin error from longitudinal:
  metric must be a valid metadata or feature table column.
Debug info has been saved to /tmp/qiime2-q2cli-err-raz8rpow.log

This is my command

qiime longitudinal pairwise-differences \
>   --m-metadata-file metadata.tsv \
>   --m-metadata-file core-metrics-results/shannon_vector.qza \
>   --p-metric shannon_vector.qza \
>   --p-group-column genotype \
>   --p-state-column age \
>   --p-state-1 8 \
>   --p-state-2 76 \
>   --p-individual-id-column batch \
>   --p-replicate-handling random \
>   --o-visualization pairwise-differences.qzv

The shannon_vector.qza is directly created from qiime diversity core-metrics-phylogenetic command. Is this wrong?

Thank you very much.

Edit:
Can I access the debug info above? I do not see tmp folder in my current working directory. Thank you again everyone.

[timanix (Timur Yergaliyev)]

@Diki

--p-metric shannon_vector.qza \

Hello, could you try to replace shannon_vector.qza with shannon_entropy and rerun it?

@Diki

Can I access the debug info above? I do not see tmp folder in my current working directory. Thank you again everyone.

You can run gedit /tmp/qiime2-q2cli-err-raz8rpow.log from the terminal. Replace gedit with other text editor if you are using another one.
Best,

[Diki (Diki P)]

Hi @timanix

It works! Thank you!
I understand now.
Another example, suppose I would like to know the pairwise comparison between sample according to their evenness (based on core-metrics-results/evenness_vector.qza file). Then they are

--m-metadata-file core-metrics-results/shannon_vector.qza \
--p-metric pielou_evenness \

Right?

Thank you very much.

[timanix (Timur Yergaliyev)]

Exactly! But you need to indicate another artifact in the core-metrics folder named corresponding to the metric you are testing. You wrote it correctly in the comment but did not change in the code part. And the metric is the name of index columns in the artifacts you are providing as an input

[Diki (Diki P)]

Oh sorry, maybe something like this then

...
--m-metadata-file core-metrics-results/shannon_vector.qza \
--p-metric pielou_evenness \
...

Just for future reference.
Thank you for your prompt help!

[timanix (Timur Yergaliyev)]

@Diki

...
--m-metadata-file core-metrics-results/evenness_vector.qza \
--p-metric pielou_evenness \
...

Here it is, the same error again

[Diki (Diki P)]

Oh yes the .qza file!
Thank you.