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