other parameters to adjust when [1] "No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR."?

[whitneyt1]

Hello!

I am running numbat on 36 lung tumor cryo visium reactions. My normal reference is a at tumor-adjacent "normal" visium reaction that has been confirmed to be tumor-free by a pathologist. My samples that I am inputting into numbat have been annotated by a pathologist and confirmed to have tumor present. Two of the samples receive the error/warning [1] "No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR." I have tried adjusting the min_LLR value, but even at 0.5, i am unable to successfully run these tissues through numbat. Do you have any advice on other parameters to adjust? Thank you!

numbat version: 1.4.1 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 = 807.8 n_cut = 0 max_iter = 2 max_nni = 100 min_depth = 0 use_loh = auto segs_loh = None call_clonal_loh = TRUE segs_consensus_fix = None multi_allelic = TRUE min_LLR = 0.5 min_overlap = 0.45 max_entropy = 0.8 skip_nj = FALSE diploid_chroms = None ncores = 20 ncores_nni = 20 common_diploid = FALSE tau = 0.2 check_convergence = FALSE plot = TRUE genome = hg38 Input metrics: 4039 cells Mem used: 1.5Gb Calling segments with clonal LOH No segments with clonal LOH detected Approximating initial clusters using smoothed expression .. Mem used: 1.5Gb number of genes left: 12443 running hclust... Iteration 1 Mem used: 6.32Gb Expression noise level (MSE): low (0.21). Running HMMs on 5 cell groups.. No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR. [1] "No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR."

[whitneyt1]

Here is what my bulk_subtrees_1.png looks like