global test and pairwise comparisons giving pvals of all NA or all 1

[jpkarl]

Hello.
Thank you for creating ANCOM BC2. I am trying to use the method to analyze species-level read counts from shotgun sequencing data from a crossover study in which I have 3 treatment groups (repeated measure) and several other factors to include in the model. I am using the code below. The results of the primary analysis look fine. However, in the global test I get W = 0 and p-val = NA for all taxa. For pairwise comparisons all p-vals = 1 (lfc and SE seem to be calculated fine).

Any guidance on what might be going wrong is appreciated. Thank you

out = ancombc2(data = phylo, fix_formula = "Treatment + Sequence + Phase", rand_formula = "(1|Subject)", p_adj_method = "BH", pseudo_sens = TRUE, prv_cut = 1, lib_cut = 0, s0_perc = 0.05, group = "Treatment", struc_zero = TRUE, neg_lb = FALSE, alpha = 0.20, n_cl = 1, verbose = TRUE, global = TRUE, pairwise = TRUE, dunnet = TRUE, trend = FALSE, iter_control = list(tol = 0.01, max_iter = 20, verbose = TRUE), em_control = list(tol = 1e-05, max_iter = 100), lme_control = lme4::lmerControl(), mdfdr_control = list(fwer_ctrl_method = "holm", B = 100), trend_control = list(contrast = NULL, node = NULL, solver = "ECOS", B = 100)

[Maggie8888]

Could you please provide more information regarding your data?