Numbat running for two samples separately but crashes when I merge the two and perform the same analysis again

[quail768]

Hey Teng,

Really amazing tool!
I am trying to run Numbat on two samples from the same patient.

I have run the Pileup and Phase script for both samples individually and Numbat seems to work when I run them individually(2 separate Numbat runs for 2 separate samples)

When I merge the two samples and try to run Numbat on the merged sample, I get the following error:

INFO [2024-08-26 11:27:34] 
numbat version: 1.4.1
scistreer version: 1.2.0
hahmmr version: 1.0.0
Running under parameters:
t = 1e-07
alpha = 1e-04
gamma = 20
min_cells = 40
init_k = 10
max_cost = 12468.9
n_cut = 6
max_iter = 2
max_nni = 100
min_depth = 0
use_loh = auto
segs_loh = None
call_clonal_loh = FALSE
segs_consensus_fix = Given
multi_allelic = TRUE
min_LLR = 5
min_overlap = 0.45
max_entropy = 0.7
skip_nj = FALSE
diploid_chroms = None
ncores = 15
ncores_nni = 15
common_diploid = TRUE
tau = 0.3
check_convergence = TRUE
plot = TRUEa
genome = hg38
Input metrics:
41563 cells
INFO [2024-08-26 11:27:35] Mem used: 10.8Gb
INFO [2024-08-26 11:28:06] Approximating initial clusters using smoothed expression ..
INFO [2024-08-26 11:28:08] Mem used: 10.8Gb
INFO [2024-08-26 13:51:18] running hclust...
INFO [2024-08-26 14:05:29] Iteration 1
INFO [2024-08-26 14:05:33] Mem used: 35.7Gb
INFO [2024-08-26 14:06:03] Expression noise level (MSE): medium (1.3). 
INFO [2024-08-26 14:06:03] Using fixed consensus CNVs
INFO [2024-08-26 14:07:56] Running HMMs on 10 cell groups..
ERROR [2024-08-26 14:08:15] No segments containing more than 10 genes for CHROM 21.
ERROR [2024-08-26 14:08:15] Error in smooth_segs(., min_genes = min_genes) : 
No segments containing more than 10 genes for CHROM 21.

I have re-ran the Pileup and Phase for both samples together as instructed in the manual.
Numbat runs for the same samples separately so I'm assuming that there are in-fact, genes for CHROM21

Any thoughts on what could be going wrong or something I could change?

Thanks for the help!

[teng-gao]

You should run pileup and phase jointly for both samples. Please check the command line options for pileup_and_phase.R for how to do this. Thanks

[quail768]

Hey @teng-gao .
Thanks for the reply.
Sorry if I was unclear.

Like I said earlier, I did run pileup and phase jointly for both samples that I planed to use for the combined Numbat run. From that single pileup and phase run, I have multiple allele_df files, all of which were included in the main Numbat run. I have run the multi-sample mode before with no problems.

Any thoughts?