Pruning stuck checking for underclustering

[doliv071]

Hi All,

I was testing out CHOIR and it was going smoothly until the last step where it got stuck trying to resolve underclustering in 1 cluster. It made 20 attempts over the course of about an hour before I killed it. Is there a parameter to control this?

> clusSCE <- CHOIR::CHOIR(clusSCE)
----------------------------------------
- CHOIR - Part 1: Build clustering tree
----------------------------------------
2025-04-09 12:00:10 PM : (Step 1/7) Checking inputs and preparing object..

Input data:
 - Object type: SingleCellExperiment
 - # of cells: 13731
 - # of batches: 1
 - # of modalities: 1
 - ATAC data: FALSE
 - Countsplitting: FALSE
 - Assay used to build tree: logcounts
 - Assay used to prune tree: logcounts

Proceeding with the following parameters:
 - Intermediate data stored under key: CHOIR
 - Alpha: 0.05
 - Multiple comparison adjustment: bonferroni
 - Features to train RF: var
 - # of excluded features: 0
 - # of permutations: 100
 - # of RF trees: 50
 - Use variance: TRUE
 - Minimum accuracy: 0.5
 - Minimum connections: 1
 - Maximum repeated errors: 20
 - Distance approximation: TRUE
 - Maximum cells sampled: Inf
 - Downsampling rate: 0.3689
 - Minimum reads: >0 reads
 - Maximum clusters: auto
 - Minimum cluster depth: 2000
 - Normalization method: none
 - Subtree dimensionality reductions: TRUE
 - Dimensionality reduction method: Default
 - Dimensionality reduction parameters provided: No
 - # of variable features: Default
 - Batch correction method: none
 - Batch correction parameters provided: No
 - Nearest neighbor parameters provided: 
     - verbose: FALSE
 - Clustering parameters provided: 
     - algorithm: 1
     - group.singletons: TRUE
     - verbose: FALSE
 - # of cores: 22
 - Random seed: 1

2025-04-09 12:00:10 PM : (Step 2/7) Running initial dimensionality reduction..
2025-04-09 12:00:10 PM : Preparing input matrix using 'logcounts' assay..
2025-04-09 12:00:18 PM : Running PCA with 2000 variable features..
2025-04-09 12:00:37 PM : (Step 3/7) Generating initial nearest neighbors graph..
2025-04-09 12:00:42 PM : (Step 4/7) Identify starting clustering resolution..
                      [[ Current tree: 6 iterations in 14s ]]                       Starting resolution: 0.001
2025-04-09 12:01:05 PM : (Step 5/7) Building root clustering tree..
                      [[ Current tree: 8 iterations in 22s ]] 
                      
                      Identified 2 clusters in root tree.
2025-04-09 12:01:30 PM : (Step 6/7) Subclustering root tree..
2025-04-09 12:01:52 PM : 10% (Subtree 1/2, 13708 cells), 2 total clusters.                             
2025-04-09 12:01:56 PM : 15% (Subtree 1/2, 13708 cells), 2 total clusters.                             
2025-04-09 12:08:35 PM : 27% (Subtree 1/2, 13708 cells), 58 total clusters.                            
2025-04-09 12:09:10 PM : 35% (Subtree 1/2, 13708 cells), 64 total clusters.                            
2025-04-09 12:11:37 PM : 42% (Subtree 1/2, 13708 cells), 90 total clusters.                            
2025-04-09 12:12:04 PM : 57% (Subtree 1/2, 13708 cells), 99 total clusters.                            
2025-04-09 12:12:06 PM : 65% (Subtree 1/2, 13708 cells), 100 total clusters.                           
2025-04-09 12:12:15 PM : 72% (Subtree 1/2, 13708 cells), 104 total clusters.                           
2025-04-09 12:12:23 PM : 87% (Subtree 1/2, 13708 cells), 108 total clusters.                           
2025-04-09 12:12:28 PM : 95% (Subtree 1/2, 13708 cells), 112 total clusters.                           
2025-04-09 12:12:30 PM : 100% (Subtree 2/2, 23 cells), 112 total clusters.                             
2025-04-09 12:12:30 PM : 100% (Subtree 2/2, 23 cells), 113 total clusters.                             
Generating subtrees.. [==============================================================] 100% in 00:10:59

2025-04-09 12:12:30 PM : (Step 7/7) Compiling full clustering tree..
                      Full tree has 75 levels and 111 clusters.

----------------------------------------
- CHOIR - Part 2: Prune clustering tree
----------------------------------------
2025-04-09 12:12:32 PM : (Step 1/2) Checking inputs and preparing object..

Input data:
 - Object type: SingleCellExperiment
 - # of cells: 13731
 - # of batches: 1
 - # of modalities: 1
 - # of subtrees: 3
 - # of levels: 75
 - # of starting clusters: 111
 - Countsplitting: FALSE
 - Assay used to build tree: logcounts
 - Assay used to prune tree: logcounts

Proceeding with the following parameters:
 - Intermediate data stored under key: CHOIR
 - Alpha: 0.05
 - Multiple comparison adjustment: bonferroni
 - Features to train RF: var
 - # of excluded features: 0
 - # of permutations: 100
 - # of RF trees: 50
 - Use variance: TRUE
 - Minimum accuracy: 0.5
 - Minimum connections: 1
 - Maximum repeated errors: 20
 - Distance approximation: TRUE
 - Distance awareness: 2
 - All metrics collected: FALSE
 - Maximum cells sampled: Inf
 - Downsampling rate: 0.3689
 - Minimum reads: >0 reads
 - Normalization method: none
 - Batch correction method: none
 - Clustering parameters provided: 
     - algorithm: 1
     - group.singletons: TRUE
     - verbose: FALSE
 - # of cores: 22
 - Random seed: 1

2025-04-09 12:12:33 PM : (Step 2/2) Iterating through clustering tree..
2025-04-09 12:13:46 PM : 10% (12/75 levels) in 1.21 min. 101 clusters remaining.                       
2025-04-09 12:15:32 PM : 20% (23/75 levels) in 2.97 min. 79 clusters remaining.                        
2025-04-09 12:17:49 PM : 30% (34/75 levels) in 5.26 min. 74 clusters remaining.                        
2025-04-09 12:19:18 PM : 40% (46/75 levels) in 6.74 min. 56 clusters remaining.                        
2025-04-09 12:21:04 PM : 50% (57/75 levels) in 8.51 min. 41 clusters remaining.                        
2025-04-09 12:26:18 PM : 60% (68/75 levels) in 13.75 min. 40 clusters remaining.                       
2025-04-09 12:28:01 PM : 70% (70/75 levels) in 15.47 min. 40 clusters remaining.                       
2025-04-09 12:33:43 PM : 81% (72/75 levels) in 21.16 min. 38 clusters remaining.                       
2025-04-09 12:34:00 PM : 90% (74/75 levels) in 21.44 min. 37 clusters remaining.                       
2025-04-09 12:34:58 PM : Additional comparisons necessary. 36 clusters remaining.                      
2025-04-09 12:35:52 PM : Additional comparisons necessary. 35 clusters remaining.                      
2025-04-09 12:36:54 PM : Additional comparisons necessary. 34 clusters remaining.                      
2025-04-09 12:37:51 PM : Additional comparisons necessary. 33 clusters remaining.                      
2025-04-09 12:37:57 PM : Checking for underclustering in 7 clusters.                                   
2025-04-09 12:38:14 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:39:32 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:41:30 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:42:45 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:44:45 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:46:09 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:48:13 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:49:29 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:51:33 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:52:49 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:54:46 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:56:04 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 12:58:15 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 12:59:39 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:01:48 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:03:12 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:05:25 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:06:51 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:09:04 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:10:26 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:12:34 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:14:02 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:16:13 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:17:37 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:19:42 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:21:05 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:22:57 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:24:14 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:26:09 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:27:25 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:29:25 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:30:43 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:32:39 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:33:54 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:35:48 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:37:06 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:39:17 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:40:48 PM : Checking for underclustering in 1 clusters.                                   
2025-04-09 01:42:59 PM : Additional comparisons necessary. 27 clusters remaining.                      
2025-04-09 01:44:25 PM : Checking for underclustering in 1 clusters. 

[cathrinesant]

Hi! I've never seen CHOIR get stuck in quite this way before. Could you check a couple things for me?

1. Does this behavior occur if you use the dev branch as well?

remotes::install_github("corceslab/CHOIR", ref = "dev", repos = BiocManager::repositories(), upgrade = "never")
# To unload a package and reload
detach("package:CHOIR", unload = TRUE)
library(CHOIR)

2. Does this behavior occur if you convert your data to a Seurat object (rather than SingleCellExperiment) and then run CHOIR?

[doliv071]

I will try a different random seed first to see if it is consistent behavior. I just wanted to check if this type of behavior was expected and I could control how hard the algo tried to solve it with some parameter before retrying. I will keep you posted

[udube]

Just FYI, I'm also having the same issue with a Seurat object. Only occurs when I'm running batch correction. I will try the dev branch and report back.

[udube]

Same issue with the dev branch but fixed when using a different random seed.

[mohdmeawad]

Nevermind, its not bonferroni related, its random seed + dataset combination - its basically random but happens often

[Landau1994]

Thanks, Try random seed like random_seed = 42 works for me

[BiotechPedro]

Hi, I got the same errors when running it in batch correction mode (embedding supplied). Basically, it's being "checking for underclustering in 1 clusters" for 12 hours. I didn't stop it yet, so I'll report back again tomorrow.

CHOIR : Version 0.3.0

set.seed(123)
seurat <- CHOIR(seurat, 
                reduction = t(sce_fit$embedding),
                var_features = rownames(seurat),
                batch_labels = "dataset_depot",
                batch_correction_method = "Harmony",
                subtree_reductions = FALSE,
                random_seed = 123, n_cores = 10)

and the output is so far:

----------------------------------------
- CHOIR - Part 1: Build clustering tree
----------------------------------------
2025-11-09 05:33:50 PM : (Step 1/7) Checking inputs and preparing object..

Input data:
 - Object type: Seurat (v5)
 - Provided inputs: reduction, var_features
 - # of cells: 113537
 - # of batches: 7
 - # of modalities: 1
 - ATAC data: FALSE
 - Countsplitting: FALSE
 - Assay: RNA
 - Layer used to build tree: data
 - Layer used to prune tree: data

Proceeding with the following parameters:
 - Intermediate data stored under key: CHOIR
 - Alpha: 0.05
 - Multiple comparison adjustment: bonferroni
 - Features to train RF: var
 - # of excluded features: 0
 - # of permutations: 100
 - # of RF trees: 50
 - Use variance: TRUE
 - Minimum accuracy: 0.5
 - Minimum connections: 1
 - Maximum repeated errors: 20
 - Distance approximation: TRUE
 - Maximum cells sampled: Inf
 - Downsampling rate: 0.3906
 - Minimum reads: >0 reads
 - Maximum clusters: auto
 - Minimum cluster depth: 2000
 - Normalization method: none
 - Subtree dimensionality reductions: FALSE
 - Dimensionality reduction method: Default
 - Dimensionality reduction parameters provided: No
 - # of variable features: 5000
 - Batch correction method: Harmony
 - Batch correction parameters provided: No
 - Metadata column containing batch information: dataset_depot
 - Nearest neighbor parameters provided: 
     - verbose: FALSE
 - Clustering parameters provided: 
     - algorithm: 1
     - group.singletons: TRUE
     - verbose: FALSE
 - # of cores: 10
 - Random seed: 123

2025-11-09 05:33:50 PM : (Step 2/7) Setting initial dimensionality reduction..
2025-11-09 05:33:50 PM : (Step 3/7) Generating initial nearest neighbors graph..
2025-11-09 05:34:19 PM : (Step 4/7) Identify starting clustering resolution..
                      Starting resolution: 0.01
2025-11-09 05:39:45 PM : (Step 5/7) Building root clustering tree..

                      
                      Identified 2 clusters in root tree.
2025-11-09 05:46:27 PM : (Step 6/7) Subclustering root tree..
2025-11-09 05:46:28 PM : 9% (Subtree 1/2, 102475 cells), 2 total clusters.
2025-11-09 05:46:54 PM : 14% (Subtree 1/2, 102475 cells), 2 total clusters.
2025-11-09 06:02:06 PM : 35% (Subtree 1/2, 102475 cells), 34 total clusters.
2025-11-09 06:13:04 PM : 52% (Subtree 1/2, 102475 cells), 40 total clusters.
2025-11-09 06:13:13 PM : 69% (Subtree 1/2, 102475 cells), 44 total clusters.
2025-11-09 06:18:05 PM : 86% (Subtree 1/2, 102475 cells), 68 total clusters.
2025-11-09 06:18:08 PM : 90% (Subtree 1/2, 102475 cells), 68 total clusters.
2025-11-09 06:18:08 PM : 91% (Subtree 2/2, 11062 cells), 68 total clusters.

2025-11-09 06:19:20 PM : (Step 7/7) Compiling full clustering tree..
                      Full tree has 44 levels and 78 clusters.

----------------------------------------
- CHOIR - Part 2: Prune clustering tree
----------------------------------------
2025-11-09 06:19:25 PM : (Step 1/2) Checking inputs and preparing object..

Input data:
 - Object type: Seurat
 - # of cells: 113537
 - # of batches: 7
 - # of modalities: 1
 - # of subtrees: 3
 - # of levels: 44
 - # of starting clusters: 78
 - Countsplitting: FALSE
 - Assay: RNA
 - Layer used to build tree: data
 - Layer used to prune tree: data

Proceeding with the following parameters:
 - Intermediate data stored under key: CHOIR
 - Alpha: 0.05
 - Multiple comparison adjustment: bonferroni
 - Features to train RF: var
 - # of excluded features: 0
 - # of permutations: 100
 - # of RF trees: 50
 - Use variance: TRUE
 - Minimum accuracy: 0.5
 - Minimum connections: 1
 - Maximum repeated errors: 20
 - Distance approximation: TRUE
 - Distance awareness: 2
 - All metrics collected: FALSE
 - Maximum cells sampled: Inf
 - Downsampling rate: 0.3906
 - Minimum reads: >0 reads
 - Normalization method: none
 - Batch correction method: Harmony
 - Metadata column containing batch information: dataset_depot
 - Clustering parameters provided: 
     - algorithm: 1
     - group.singletons: TRUE
     - verbose: FALSE
 - # of cores: 10
 - Random seed: 123

2025-11-09 06:19:32 PM : (Step 2/2) Iterating through clustering tree..
2025-11-09 06:21:31 PM : 10% (7/44 levels) in 1.97 min. 72 clusters remaining.
2025-11-09 06:49:56 PM : 20% (14/44 levels) in 30.4 min. 67 clusters remain...
2025-11-09 07:36:00 PM : 27% (19/44 levels) in 76.46 min. 56 clusters remai...
2025-11-09 07:43:20 PM : 30% (21/44 levels) in 83.79 min. 56 clusters remai...
2025-11-09 07:46:11 PM : 40% (27/44 levels) in 86.64 min. 48 clusters remai...
2025-11-09 07:47:51 PM : 50% (34/44 levels) in 88.31 min. 40 clusters remai...
2025-11-09 08:07:54 PM : 60% (40/44 levels) in 108.36 min. 30 clusters rema...
2025-11-09 08:26:33 PM : 70% (41/44 levels) in 127.01 min. 27 clusters rema...
2025-11-09 08:31:04 PM : 80% (42/44 levels) in 131.53 min. 26 clusters rema...
2025-11-09 08:42:29 PM : 90% (44/44 levels) in 142.94 min. 25 clusters rema...
2025-11-09 08:46:12 PM : Additional comparisons necessary. 24 clusters rema...
2025-11-09 08:50:31 PM : Additional comparisons necessary. 23 clusters rema...
2025-11-09 08:55:19 PM : Checking for underclustering in 4 clusters.
2025-11-09 08:59:40 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 09:08:21 PM : Checking for underclustering in 1 clusters.
2025-11-09 09:11:41 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 09:20:14 PM : Checking for underclustering in 1 clusters.
2025-11-09 09:23:33 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 09:32:06 PM : Checking for underclustering in 1 clusters.
2025-11-09 09:35:29 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 09:44:03 PM : Checking for underclustering in 1 clusters.
2025-11-09 09:47:32 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 09:56:02 PM : Checking for underclustering in 1 clusters.
2025-11-09 09:59:21 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 10:07:57 PM : Checking for underclustering in 1 clusters.
2025-11-09 10:11:11 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 10:19:46 PM : Checking for underclustering in 1 clusters.
2025-11-09 10:23:03 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 10:31:37 PM : Checking for underclustering in 1 clusters.
2025-11-09 10:35:01 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 10:43:35 PM : Checking for underclustering in 1 clusters.
2025-11-09 10:47:04 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 10:55:42 PM : Checking for underclustering in 1 clusters.
2025-11-09 10:59:15 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 11:07:56 PM : Checking for underclustering in 1 clusters.
2025-11-09 11:11:37 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 11:20:07 PM : Checking for underclustering in 1 clusters.
2025-11-09 11:23:43 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 11:32:17 PM : Checking for underclustering in 1 clusters.
2025-11-09 11:35:50 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 11:44:21 PM : Checking for underclustering in 1 clusters.
2025-11-09 11:47:59 PM : Additional comparisons necessary. 20 clusters rema...
2025-11-09 11:56:37 PM : Checking for underclustering in 1 clusters.
2025-11-10 12:00:17 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 12:08:54 AM : Checking for underclustering in 1 clusters.
2025-11-10 12:12:42 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 12:21:23 AM : Checking for underclustering in 1 clusters.
2025-11-10 12:25:25 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 12:34:03 AM : Checking for underclustering in 1 clusters.
2025-11-10 12:37:17 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 12:45:55 AM : Checking for underclustering in 1 clusters.
2025-11-10 12:49:09 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 12:57:44 AM : Checking for underclustering in 1 clusters.
2025-11-10 01:00:59 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 01:09:33 AM : Checking for underclustering in 1 clusters.
2025-11-10 01:12:51 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 01:21:28 AM : Checking for underclustering in 1 clusters.
2025-11-10 01:24:53 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 01:33:30 AM : Checking for underclustering in 1 clusters.
2025-11-10 01:36:59 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 01:45:37 AM : Checking for underclustering in 1 clusters.
2025-11-10 01:49:11 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 01:57:50 AM : Checking for underclustering in 1 clusters.
2025-11-10 02:01:31 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 02:10:00 AM : Checking for underclustering in 1 clusters.
2025-11-10 02:13:39 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 02:22:11 AM : Checking for underclustering in 1 clusters.
2025-11-10 02:25:43 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 02:34:14 AM : Checking for underclustering in 1 clusters.
2025-11-10 02:37:52 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 02:46:27 AM : Checking for underclustering in 1 clusters.
2025-11-10 02:50:08 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 02:58:49 AM : Checking for underclustering in 1 clusters.
2025-11-10 03:02:37 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 03:11:19 AM : Checking for underclustering in 1 clusters.
2025-11-10 03:15:21 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 03:24:02 AM : Checking for underclustering in 1 clusters.
2025-11-10 03:27:15 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 03:35:51 AM : Checking for underclustering in 1 clusters.
2025-11-10 03:39:05 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 03:47:40 AM : Checking for underclustering in 1 clusters.
2025-11-10 03:50:54 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 03:59:30 AM : Checking for underclustering in 1 clusters.
2025-11-10 04:02:47 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 04:11:21 AM : Checking for underclustering in 1 clusters.
2025-11-10 04:14:45 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 04:23:22 AM : Checking for underclustering in 1 clusters.
2025-11-10 04:26:52 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 04:35:29 AM : Checking for underclustering in 1 clusters.
2025-11-10 04:39:03 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 04:48:05 AM : Checking for underclustering in 1 clusters.
2025-11-10 04:51:47 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 05:00:40 AM : Checking for underclustering in 1 clusters.
2025-11-10 05:04:17 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 05:13:12 AM : Checking for underclustering in 1 clusters.
2025-11-10 05:16:45 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 05:25:40 AM : Checking for underclustering in 1 clusters.
2025-11-10 05:29:20 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 05:38:15 AM : Checking for underclustering in 1 clusters.
2025-11-10 05:41:59 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 05:50:58 AM : Checking for underclustering in 1 clusters.
2025-11-10 05:54:48 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 06:03:55 AM : Checking for underclustering in 1 clusters.
2025-11-10 06:08:00 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 06:16:58 AM : Checking for underclustering in 1 clusters.
2025-11-10 06:20:14 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 06:29:10 AM : Checking for underclustering in 1 clusters.
2025-11-10 06:32:24 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 06:41:20 AM : Checking for underclustering in 1 clusters.
2025-11-10 06:44:36 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 06:53:32 AM : Checking for underclustering in 1 clusters.
2025-11-10 06:56:53 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 07:05:48 AM : Checking for underclustering in 1 clusters.
2025-11-10 07:09:15 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 07:18:15 AM : Checking for underclustering in 1 clusters.
2025-11-10 07:21:47 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 07:30:46 AM : Checking for underclustering in 1 clusters.
2025-11-10 07:34:23 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 07:43:25 AM : Checking for underclustering in 1 clusters.
2025-11-10 07:47:07 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 07:55:59 AM : Checking for underclustering in 1 clusters.
2025-11-10 07:59:37 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 08:08:31 AM : Checking for underclustering in 1 clusters.
2025-11-10 08:12:05 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 08:21:02 AM : Checking for underclustering in 1 clusters.
2025-11-10 08:24:42 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 08:33:37 AM : Checking for underclustering in 1 clusters.
2025-11-10 08:37:20 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 08:46:26 AM : Checking for underclustering in 1 clusters.
2025-11-10 08:50:15 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 08:59:21 AM : Checking for underclustering in 1 clusters.
2025-11-10 09:03:23 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 09:12:25 AM : Checking for underclustering in 1 clusters.
2025-11-10 09:15:41 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 09:24:36 AM : Checking for underclustering in 1 clusters.
2025-11-10 09:27:50 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 09:36:45 AM : Checking for underclustering in 1 clusters.
2025-11-10 09:40:01 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 09:48:56 AM : Checking for underclustering in 1 clusters.
2025-11-10 09:52:16 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 10:01:11 AM : Checking for underclustering in 1 clusters.
2025-11-10 10:04:35 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 10:13:32 AM : Checking for underclustering in 1 clusters.
2025-11-10 10:17:03 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 10:26:04 AM : Checking for underclustering in 1 clusters.
2025-11-10 10:29:39 AM : Additional comparisons necessary. 20 clusters rema...
2025-11-10 10:38:41 AM : Checking for underclustering in 1 clusters.
2025-11-10 10:42:23 AM : Additional comparisons necessary. 20 clusters rema...

Hope it's useful. Thanks!

[BiotechPedro]

Hi again.

I just run it with same parameters and dataset, but a different seed (42). It worked!