Error in find_common_diploid(bulks, gamma = gamma, alpha = alpha, ncores = ncores) : Error in smooth_segs(., min_genes = min_genes) :

[whitneyt1]

`> #Run Numbat

out=run_numbat(count_mat = mat_clean,

•            lambdas_ref = numbat_ref_N2535,
  

•            df_allele = df_allele,
  

•            genome = 'hg38',
  

•            t=1e-5,
  

•            max_entropy = 0.8,
  

•            ncores=4,
  

•            plot = TRUE,
  

•            out_dir = './Numbat_Outs/outs/'
  

• )

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 = 1246.2
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 = 0.8
skip_nj = FALSE
diploid_chroms = None
ncores = 4
ncores_nni = 4
common_diploid = TRUE
tau = 0.3
check_convergence = FALSE
plot = TRUE
genome = hg38
Input metrics:
4154 cells
Mem used: 2.16Gb
Approximating initial clusters using smoothed expression ..
Mem used: 2.16Gb
number of genes left: 12099
running hclust...
! # Invaild edge matrix for . A <tbl_df> is returned.
! # Invaild edge matrix for . A <tbl_df> is returned.
Iteration 1
Mem used: 7.2Gb
High SNP contamination detected (72.9%). Please make sure that cells from only one individual are included in genotyping step.
Expression noise level (MSE): medium (1.4).
Running HMMs on 5 cell groups..
Error in find_common_diploid(bulks, gamma = gamma, alpha = alpha, ncores = ncores) :
Error in smooth_segs(., min_genes = min_genes) :
No segments containing more than 10 genes for CHROM 13,21.
In addition: Warning message:
In mclapply(bulks %>% split(.$sample), mc.cores = ncores, function(bulk) { :
scheduled cores 2, 1 encountered errors in user code, all values of the jobs will be affected`

Hello, I am getting this error once run_numbat begins trying to run HMMs.

I am using numbat on a series of 10X Visium lung cancer tissues. my normal reference is a normal lung tissues 10X visium reaction. I have ensured the gene names are in the same format between the reference and test.

This is the script i used to loop through reactions to perform the pileup step.

Thank you!

[whitneyt1]

Hello, I have been unable to address this issue still. Is there any additional information I can provide? @teng-gao

[teng-gao]

Hello, if your Visium data is probed based chemistry Numbat doesn’t support this

[whitneyt1]

hi @teng-gao it is not probe based, it is 3' sequencing on frozen sections. Thanks!

[teng-gao]

Seems that the SNP profile looks aberrant:

High SNP contamination detected (72.9%). Please make sure that cells from only one individual are included in genotyping step.

It's hard to tell what the issue is however only based on this message ..

[whitneyt1]

Thank you, @teng-gao
these visium reactions are individual patient tumors. Is there any additional information I can provide that would be helpful to deduce the issue? thanks!

[whitneyt1]

I identified that I was following the mouse tutorial for human spatial data and did not phase my human data appropriately as per the "Getting Started" vignette. After running pileup_and_phase.R correctly, it resolved this issue.