ancombc2 output fmt length exceeds maximal format length 8192

[Hesham999666]

I tried to do an ancombc2 comparison between 2 groups on a genus level. When I don't filter out low abundance taxa or using filter down taxa below 0.01%. Only the ancombc2 function work when I use 0.1% filter.

It used to work before with same phyloseq object ! What could possible went wrong here

output.apnea = ancombc2(data = ps2, assay_name = "counts", tax_level = "Genus", fix_formula = "apnea453", rand_formula = NULL, p_adj_method = "holm", pseudo = 0, pseudo_sens = FALSE, prv_cut = 0.01, lib_cut = 0, s0_perc = 0.05, group = NULL, struc_zero = FALSE , neg_lb = FALSE, alpha = 0.05, n_cl = 2, verbose = TRUE, global = FALSE, pairwise = FALSE, dunnet = FALSE, trend = FALSE, iter_control = list(tol = 1e-2, max_iter = 5,verbose = FALSE), em_control = list(tol = 1e-5, max_iter = 5), lme_control = lme4::lmerControl(), mdfdr_control = list(fwer_ctrl_method = "holm", B = 1), trend_control = list(contrast = list(matrix(c(1, 0, -1, 1), nrow = 2, byrow = TRUE), matrix(c(-1, 0, 1, -1), nrow = 2, byrow = TRUE)), node = list(2, 2), solver = "ECOS", B = 5))

[Maggie8888]

Your samples may have an excessive number of zero values if you do not filer them down. This will cause an issue while conducting unbiased estimation.

[Hesham999666]

Thanks for your answer.

Is there is way, hopefully a code I can use it with the phyloseq object I have to fix this problem ?