Fail during numbat : object 'seg' not found

[sxf-ux]

hi. I received an error with one of my runs. Here is the log file:

``
numbat version: 1.4.0
scistreer version: 1.2.0
hahmmr version: 1.0.0
Running under parameters:
t = 1e-05
alpha = 1e-04
gamma = 20
min_cells = 50
init_k = 3
max_cost = 3422.7
n_cut = 0
max_iter = 2
max_nni = 100
min_depth = 0
use_loh = auto
segs_loh = None
call_clonal_loh = FALSE
segs_consensus_fix = None
multi_allelic = TRUE
min_LLR = 5
min_overlap = 0.45
max_entropy = 0.5
skip_nj = FALSE
diploid_chroms = None
ncores = 4
ncores_nni = 16
common_diploid = TRUE
tau = 0.3
check_convergence = FALSE
plot = TRUE
genome = hg38
Input metrics:
11409 cells
Mem used: 2.44Gb
Approximating initial clusters using smoothed expression ..
Mem used: 2.44Gb
number of genes left: 9506
running hclust...
Iteration 1
Mem used: 12.7Gb
Expression noise level (MSE): high (2.8). Consider using a custom expression reference profile.
Running HMMs on 5 cell groups..
Retesting CNVs..
Retesting CNVs..
Retesting CNVs..
Retesting CNVs..
Retesting CNVs..
Running HMMs on 3 cell groups..
Testing for multi-allelic CNVs ..
0 multi-allelic CNVs found:
Evaluating CNV per cell ..
Mem used: 5.13Gb
All cells succeeded
Expanding allelic states..
No multi-allelic CNVs, skipping ..
No multi-allelic CNVs, skipping ..
No multi-allelic CNVs, skipping ..
Building phylogeny ..
Mem used: 5.21Gb
Using 1 CNVs to construct phylogeny
Using NJ tree as seed..
Mem used: 5.74Gb
Iter 2 -1352.26392982027, 0.34s
Iter 3 -1352.26392982027, 0.3s
Found 6588 normal cells..
Iteration 2
Mem used: 5.78Gb
Running HMMs on 2 cell groups..
Retesting CNVs..
Retesting CNVs..
Running HMMs on 2 cell groups..
Testing for multi-allelic CNVs ..
0 multi-allelic CNVs found:
Evaluating CNV per cell ..
Mem used: 5.37Gb
All cells succeeded
Error in mutate():
i In argument: `seg = factor(seg, mixedsort(unique(seg)))`.
Caused by error:
! object 'seg' not found
Backtrace:
x

1. +-numbat::run_numbat(...)
2. | -numbat:::get_exp_post(...)
3. | -... %>% ...
4. +-dplyr::mutate(., seg_label = factor(seg_label, unique(seg_label)))
5. +-dplyr::mutate(., seg_label = paste0(seg, "(", cnv_state, ")"))
6. +-numbat:::compute_posterior(.)
7. | -... %>% ungroup()
8. +-dplyr::ungroup(.)
9. +-dplyr::mutate(...)
10. +-dplyr::rowwise(.)
11. +-dplyr::mutate_at(...)
12. | -dplyr:::manip_at(...)
13. | -dplyr:::tbl_at_syms(...)
14. | -dplyr:::tbl_at_vars(...)
15. | -dplyr::tbl_vars(tbl)
16. | +-dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
17. | | -base::structure(...)
18. | -dplyr:::tbl_vars_dispatch(x)
19. +-dplyr::left_join(...)
20. +-dplyr::mutate(., seg = factor(seg, mixedsort(unique(seg))))
21. +-dplyr:::mutate.data.frame(., seg = factor(seg, mixedsort(unique(seg))))
22. | -dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
23. | +-base::withCallingHandlers(...)
24. | -dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
25. | -mask$eval_all_mutate(quo)
26. | -dplyr (local) eval()
27. +-base::factor(seg, mixedsort(unique(seg)))
28. -base::.handleSimpleError(<fn>, "object 'seg' not found", base::quote(NULL))
29. -dplyr (local) h(simpleError(msg, call))

30. \-rlang::abort(message, class = error_class, parent = parent, call = error_call)
    

Warning messages:
1: In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.2 GiB
2: In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.7 GiB
3: In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.7 GiB
4: In mclapply(cells, mc.cores = ncores, function(cell) { :
scheduled cores 1, 2, 3, 4 did not deliver results, all values of the jobs will be affected
Execution halted
``