error with run_lefse with 1 group and one subgroup: Error in `purrr::map2_lgl()`: i In index: 1

[nadiaandreani]

Hi, I am using MicrobiomeMarker to run lefse on my dataset. Briefly I am looking at fecal microbiome in patients and controls from 3 locations.

The command works if I use 2 independent analyses (one for condition, one for location), but when using "group" and "subgroup" I get an error. Here my code and following issue:

lefse_locANDcondition <- normalize(df, method = "CPM") %>%

• run_lefse(
• wilcoxon_cutoff = 0.01,
• norm = "none", # must be "none" since the input has been normalized
• group ="group",
• subgroup = "location",
• kw_cutoff = 0.01,
• multigrp_strat = TRUE,
• lda_cutoff = 4,
• taxa_rank = "Species"

• ) Error in purrr::map2_lgl(): i In index: 1. i With name: Blautia_producta. Caused by error in if ((sx < sy) != dir_cmp || sx == sy) ...: ! missing value where TRUE/FALSE needed Run rlang::last_error() to see where the error occurred. rlang::last_error() <error/purrr_error_indexed> Error in purrr::map2_lgl(): i In index: 1. i With name: Blautia_producta. Caused by error in if ((sx < sy) != dir_cmp || sx == sy) ...: ! missing value where TRUE/FALSE needed

  Backtrace:

  1. normalize(df, method = "CPM") %>% ...
  2. microbiomeMarker::run_lefse(...)
  3. purrr::map2_lgl(...)
  4. purrr:::map2_("logical", .x, .y, .f, ..., .progress = .progress)
  5. microbiomeMarker (local) .f(.x[[i]], .y[[i]], ...)
  6. microbiomeMarker:::test_rep_wilcoxon(...) Run rlang::last_trace() to see the full context.

Can you help me troubleshooting?

Thanks in advance,

Nadia