INFO [2024-05-13 09:47:20] 
numbat version: 1.4.0
scistreer version: 1.2.0
hahmmr version: 1.0.0
Running under parameters:
t = 0.00001
alpha = 0.0001
gamma = 20
min_cells = 50
init_k = 3
max_cost = 2310.6
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 = 16
ncores_nni = 16
common_diploid = TRUE
tau = 0.3
check_convergence = FALSE
plot = TRUE
genome = hg38
Input metrics:
7702 cells
INFO [2024-05-13 09:47:20] Mem used: 1.99Gb
INFO [2024-05-13 09:47:34] Approximating initial clusters using smoothed expression ..
INFO [2024-05-13 09:47:34] Mem used: 1.99Gb
INFO [2024-05-13 09:55:01] running hclust...
INFO [2024-05-13 10:08:20] Iteration 1
INFO [2024-05-13 10:08:22] Mem used: 10.9Gb
INFO [2024-05-13 10:08:40] Expression noise level (MSE): high (3.4). Consider using a custom expression reference profile.
INFO [2024-05-13 10:08:41] Running HMMs on 5 cell groups..
INFO [2024-05-13 10:09:07] diploid regions: 1b,2b,3a,3c,3e,3g,3i,9b,10a,10c,12b,12d,16b,20a
INFO [2024-05-13 10:14:22] Running HMMs on 3 cell groups..
INFO [2024-05-13 10:14:46] diploid regions: 1e,2b,3a,3c,3e,3g,3i,9b,10a,10c,12b,12d,16b,20a
INFO [2024-05-13 10:17:25] Testing for multi-allelic CNVs ..
INFO [2024-05-13 10:17:26] 5 multi-allelic CNVs found: 11a,19a,19i,1d,22a
INFO [2024-05-13 10:17:26] Evaluating CNV per cell ..
INFO [2024-05-13 10:17:27] Mem used: 6.22Gb
INFO [2024-05-13 11:26:35] All cells succeeded
INFO [2024-05-13 11:29:59] Expanding allelic states..
INFO [2024-05-13 11:31:36] Building phylogeny ..
INFO [2024-05-13 11:31:37] Mem used: 6.84Gb
INFO [2024-05-13 11:31:37] Using 32 CNVs to construct phylogeny
INFO [2024-05-13 11:54:00] Using UPGMA tree as seed..
INFO [2024-05-13 11:54:01] Mem used: 7.22Gb
INFO [2024-05-13 11:58:44] opt_move:10b->7a, cost=2.78
INFO [2024-05-13 11:58:44] opt_move:13a->5d, cost=4.18
INFO [2024-05-13 11:58:44] opt_move:8b->1d_bdel, cost=8.53
INFO [2024-05-13 11:58:44] opt_move:19a_bdel->19i_bdel, cost=13.9
INFO [2024-05-13 11:58:44] opt_move:6d->19h, cost=14.6
INFO [2024-05-13 11:58:44] opt_move:11c->17a, cost=17.8
INFO [2024-05-13 11:58:44] opt_move:2a->1a,6a, cost=25.5
INFO [2024-05-13 11:58:44] opt_move:4d->13a,5d, cost=29.7
INFO [2024-05-13 11:58:45] opt_move:15a->2d, cost=40.7
INFO [2024-05-13 11:58:45] opt_move:1b->15a,2d, cost=88.1
INFO [2024-05-13 11:58:45] opt_move:1d_bdel,8b->1a,6a,2a, cost=99.2
INFO [2024-05-13 11:58:45] opt_move:10b,7a->22a_del, cost=282
INFO [2024-05-13 11:58:45] opt_move:10b,7a,22a_del->19h,6d, cost=350
INFO [2024-05-13 11:58:45] opt_move:5e->19a_bdel,19i_bdel, cost=424
INFO [2024-05-13 11:58:45] opt_move:22a_bdel->11a_bdel, cost=1250
INFO [2024-05-13 11:58:45] opt_move:11a_bdel,22a_bdel->1a,6a,2a,1d_bdel,8b, cost=1090
INFO [2024-05-13 11:58:45] opt_move:11c,17a->13a,5d,4d, cost=1820
INFO [2024-05-13 11:59:12] Found 268 normal cells..
INFO [2024-05-13 11:59:31] Iteration 2
INFO [2024-05-13 11:59:32] Mem used: 7.52Gb
INFO [2024-05-13 11:59:55] Running HMMs on 13 cell groups..
INFO [2024-05-13 12:00:32] diploid regions: 3a,10a,16b,20a
INFO [2024-05-13 12:08:18] Running HMMs on 10 cell groups..
INFO [2024-05-13 12:08:41] diploid regions: 1c,3a,10a,16b,20a
INFO [2024-05-13 12:11:45] Testing for multi-allelic CNVs ..
INFO [2024-05-13 12:11:45] 2 multi-allelic CNVs found: 19i,1c
INFO [2024-05-13 12:11:46] Evaluating CNV per cell ..
INFO [2024-05-13 12:11:47] Mem used: 10.6Gb
INFO [2024-05-13 12:59:05] All cells succeeded
INFO [2024-05-13 13:01:48] Expanding allelic states..
INFO [2024-05-13 13:02:23] Building phylogeny ..
INFO [2024-05-13 13:02:24] Mem used: 10.4Gb
INFO [2024-05-13 13:02:24] Using 21 CNVs to construct phylogeny
INFO [2024-05-13 13:13:43] Using UPGMA tree as seed..
INFO [2024-05-13 13:13:44] Mem used: 10.4Gb
INFO [2024-05-13 13:16:31] opt_move:15a->6c, cost=0.43
INFO [2024-05-13 13:16:31] opt_move:8a->11f, cost=1.13
INFO [2024-05-13 13:16:31] opt_move:4d->17a, cost=16
INFO [2024-05-13 13:16:31] opt_move:19a->11c, cost=25.6
INFO [2024-05-13 13:16:31] opt_move:13a->17a,4d, cost=41.6
INFO [2024-05-13 13:16:31] opt_move:7a->15a,6c, cost=67.4
INFO [2024-05-13 13:16:32] opt_move:22a->11c,19a, cost=224
INFO [2024-05-13 13:16:32] opt_move:5c->13a,17a,4d, cost=272
INFO [2024-05-13 13:16:32] opt_move:15a,6c,7a->11f,8a, cost=272
INFO [2024-05-13 13:16:32] opt_move:3b->11f,8a,15a,6c,7a, cost=472
INFO [2024-05-13 13:16:32] opt_move:9b->11f,8a,15a,6c,7a,3b, cost=479
INFO [2024-05-13 13:16:32] opt_move:19i_bdel->11c,19a,22a, cost=895
INFO [2024-05-13 13:16:32] opt_move:11a->1a, cost=1030
INFO [2024-05-13 13:16:56] Found 2286 normal cells..
INFO [2024-05-13 13:17:27] Running HMMs on 9 cell groups..
INFO [2024-05-13 13:17:37] diploid regions: 1g,2c,3a,6a,7a,8c,9a,10a,12a,19b
INFO [2024-05-13 13:17:38] quadruploid state enabled
INFO [2024-05-13 13:17:38] diploid regions: 1a,11a,12a,14a,16b,17a,19a,20a,21a,22a
INFO [2024-05-13 13:17:40] quadruploid state enabled
INFO [2024-05-13 13:17:40] diploid regions: 1a,1c,1e,4b,8a,9b,12a,15a,16a,20a,21a
INFO [2024-05-13 13:17:42] quadruploid state enabled
INFO [2024-05-13 13:17:42] diploid regions: 1a,11a,14a,16b,17a,19a,20a,21a,22a
INFO [2024-05-13 13:17:43] quadruploid state enabled
INFO [2024-05-13 13:17:43] diploid regions: 1a,8a,9a,11b,11d,11f,12a,12c,12e,14a,16a,17a,19a,19c,20a,21a,22a
INFO [2024-05-13 13:17:45] diploid regions: 1a,1c,1e,3a,4c,6b,8a,8d,9b,10a,12b,12d,16a,20a,21a
INFO [2024-05-13 13:17:45] diploid regions: 1b,1d,2b,2d,3a,3c,3e,6b,9a,10a,12a,12c,12e,14a,16b,18a,19b,19d,20a
INFO [2024-05-13 13:17:45] quadruploid state enabled
INFO [2024-05-13 13:17:45] diploid regions: 1b,2d,3a,3c,3e,3g,4b,6b,9a,10a,12a,12c,12e,14b,16b,18a,19b,19d,20a
INFO [2024-05-13 13:17:47] quadruploid state enabled
INFO [2024-05-13 13:17:47] diploid regions: 1a,1c,2b,9b,12a,14b,16a,19d,20a,21b
INFO [2024-05-13 13:21:11] All done!