Correct --p-metric parameter for beta diversity metric use in qiime longitudinal pairwaise-differences

[Alessandro_Lazzaro]

Dear Developers,
I am trying to use the qiime longitudinal plugin applying the pairwise-differences visualizer to parse microbiome differences between two groups and along two time-points (before and after treatment).
Unfortunately, I am having the same issue reported in the following post (whose question remained unsolved, from my understanding):

Question about qiime longitudinal pairwise-differences

Dear User Support, I am trying to use Mann-Whitney U test through qiime longitudinal pairwise-differences to compare two sample types within each individual (Individual_ID), repeated by 18 individuals. I set Individual_ID column as group-column, since –p-group-column: Metadata column on which to separate groups for comparison [required]: qiime longitudinal pairwise-differences –m-metadata-file MetaData.tsv –m-metadata-file core-metrics-results/shannon_vector.qza –p-metric shannon –p-g…

that is, when I try to use a beta diversity metric to comparison, I am not able to insert the right --p-metric label.

This is my code:
qiime longitudinal pairwise-differences
--m-metadata-file COHORT_A_LESS_LOST_FU2.txt
--m-metadata-file unweighted_unifrac_pcoa_results.qza
--p-metric Axis 1
--p-group-column Arm
--p-state-column MONTH
--p-state-1 0
--p-state-2 6
--p-individual-id-column studyid
--p-replicate-handling random
--o-visualization pairwise-differences_unweighted.qzv
And this is the error, independently of the use of --verbose at the end of the code:
(1/1) Got unexpected extra argument (1)

If I try to use "Axis 1" or 'Axis 1' I receive this error:
Error: Detected invalid character in: ‘Axis, 1’
Verify the correct quotes or dashes (ASCII) are being used.
or
Error: Detected invalid character in: “Axis, 1”
Verify the correct quotes or dashes (ASCII) are being used.
respectively.

I am using the qiime2-2020.2 version on a McBookPro.
Thank you in advance for your help,
Alessandro Lazzaro

[Zach_Burcham]

If I am not mistaken, I believe you have to put quotes around Axis 1 if you use it as an input. I also think the pairwise-differences function only works for alpha diversity metrics and for beta diversity metrics you would need to use pairwise-distances.

[Nicholas_Bokulich]

Welcome @Alessandro_Lazzaro!

@Zach_Burcham is correct, you need to put quotes around "Axis 1". I see that you tried that already:

@Alessandro_Lazzaro

Error: Detected invalid character in: ‘Axis, 1’
Verify the correct quotes or dashes (ASCII) are being used.

That sounds like exactly what it is saying: an invalid character was detected. Sounds like you were probably copying/pasting into the terminal from another source (website, document) that may have hidden formatting... my advice is to try typing it into the terminal from scratch.

Good luck and thanks @Zach_Burcham!

[Alessandro_Lazzaro]

Oh, thank you for the tip: it worked!