diversity alpha (faiths_pd) generating NA when other metrics do not and phylogeny is complete

Technical Support
1

Hello - I'm hoping someone can help clear this up for me because I'm been banging my head against the wall for a while trying to figure this out. I can't find any similar issues, so it's likely something on my end but I wanted to check.

I'm running amplicon-2024.10 on an Apple-chipped MacBook Pro.

I'm experiencing an issue where I'm getting NAs for certain samples when running Faith's PD, but values when running non-phylogenetic metrics such as observed_features and shannon. I'm not getting any error (!), including those related to features present in the table not being present in the phylogeny. I typically compare across metrics, and have never seen this before. I was able to reproduce this with a 16S tree/table and a shotgun tree/table. Thanks in advance for any insight

Command run:
qiime diversity alpha-phylogenetic
--i-table /Users/shaffer-local/Mycelia/Academia/Projects/matrix/data/shotgun/matrix_shotgun_wolr2pe_gg2_biom_lbm_noControls_noSingletons_rar89K.qza
--i-phylogeny /Users/shaffer-local/Mycelia/Bioinformatics/databases/wol/wol_r2/wolr2_phylogeny.qza
--p-metric faith_pd
--o-alpha-diversity /Users/shaffer-local/Mycelia/Academia/Projects/matrix/data/shotgun/matrix_shotgun_wolr2pe_gg2_biom_lbm_noControls_noSingletons_rar89K_alpha_faithspd.qza

2

Hello Justin,

Can you post the date you used to replicate? Perhaps one of the phylogeny devs can take a look at this and check for bugs.

I understand if some data can not be shared. Only post what's right for you.

3

Hello. Thanks for your reply. I was able to replicate this with both the GreenGenes 2 phylogeny (16S) and the Web of Life Toolkit App (Woltka) phylogeny (metagenomics). Both trees are too big to post here, but I've linked them below.

GG2:
http://ftp.microbio.me/greengenes_release/current/

Woltka:

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