Error in hclust(dist_mat, method = "ward.D2") : size cannot be NA nor exceed 65536

[YiweiNiu]

Hi,

I am testing numbat on one patient with 68941 cells, and it ended with the following error:

Numbat version: 1.3.2.1
Scistreer version: 1.2.0
Running under parameters:
t = 1e-05
alpha = 1e-04
gamma = 20
min_cells = 50
init_k = 3
max_cost = 20682.3
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 = 14
ncores_nni = 14
common_diploid = TRUE
tau = 0.3
check_convergence = FALSE
plot = TRUE
genome = hg38
Input metrics:
68941 cells
Mem used: 22.3Gb
Approximating initial clusters using smoothed expression ..
Mem used: 22.3Gb
number of genes left: 10197
running hclust...
Error in hclust(dist_mat, method = "ward.D2") : 
  size cannot be NA nor exceed 65536
Calls: run_numbat -> exp_hclust -> hclust
In addition: Warning messages:
1: In asMethod(object) :
  sparse->dense coercion: allocating vector of size 7.1 GiB
2: In asMethod(object) :
  sparse->dense coercion: allocating vector of size 5.2 GiB
Execution halted

I found this thread after searching: Greater than 65536 observations. It seems like a limitation of hclust.

Best regards,
Yiwei