=== STDOUT ===
05:46:31 Experiment 10 (expanded): scIB Metric Construct-Validity Audit
05:46:31 Prereg: PREREGISTRATION_SCIB_EXPANDED_PANEL.md
05:46:31 Census: 2023-12-15
05:46:31 Tissues: ['lung', 'liver', 'kidney', 'brain']
05:46:31 Seed: 20260713
05:46:31 Metrics: ['nmi_leiden', 'ari_leiden', 'silhouette_label', 'clisi', 'isolated_label_asw', 'silhouette_batch', 'ilisi', 'kbet', 'graph_connectivity', 'pcr_comparison']
05:46:31 Real embeddings (Census): ['geneformer', 'scvi', 'scgpt', 'uce']
05:46:31 Phase 2b models: ['geneformer_v2_104m', 'geneformer_v2_316m', 'scprint', 'nicheformer']
05:46:31 Phase 2b dir: results/embeddings

============================================================
05:46:38 Processing tissue: lung
05:46:38 Pulling source cells...
  Source: 2000 cells
05:49:24 Pulling target cells...
  Target: 2000 cells
  geneformer: d=512
  scvi: d=50
  scgpt: d=512
  uce: d=1280
  geneformer_v2_104m: loaded from .npy, d=768
  geneformer_v2_316m: loaded from .npy, d=1152
  scprint: .npy not found for lung, skipping
  nicheformer: .npy not found for lung, skipping

05:51:36 Computing scIB metrics: lung / geneformer (d=512)
  05:51:54 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  05:54:27 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.466
    nmi_leiden: 0.6939 [OK]
    ari_leiden: 0.3730 [OK]
    silhouette_label: 0.4868 [OK]
    silhouette_batch: 0.7807 [OK]
    isolated_label_asw: 0.5331 [OK]
    graph_connectivity: 0.7633 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9933 [OK]
    ilisi: 0.0050 [OK]
    kbet: N/A [N/A]

05:54:43 Computing scIB metrics: lung / scvi (d=50)
  05:54:45 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  05:56:29 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.327
    nmi_leiden: 0.6558 [OK]
    ari_leiden: 0.3693 [OK]
    silhouette_label: 0.4338 [OK]
    silhouette_batch: 0.7704 [OK]
    isolated_label_asw: 0.5052 [OK]
    graph_connectivity: 0.7431 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9878 [OK]
    ilisi: 0.1266 [OK]
    kbet: N/A [N/A]

05:56:32 Computing scIB metrics: lung / scgpt (d=512)
  05:56:33 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  05:58:16 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.257
    nmi_leiden: 0.6356 [OK]
    ari_leiden: 0.3391 [OK]
    silhouette_label: 0.4400 [OK]
    silhouette_batch: 0.6929 [OK]
    isolated_label_asw: 0.5305 [OK]
    graph_connectivity: 0.7588 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9902 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

05:58:22 Computing scIB metrics: lung / uce (d=1280)
  05:58:24 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:00:17 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.365
    nmi_leiden: 0.6846 [OK]
    ari_leiden: 0.3048 [OK]
    silhouette_label: 0.5038 [OK]
    silhouette_batch: 0.6867 [OK]
    isolated_label_asw: 0.5559 [OK]
    graph_connectivity: 0.7117 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9945 [OK]
    ilisi: 0.0021 [OK]
    kbet: N/A [N/A]

06:00:26 Computing scIB metrics: lung / random_projection (d=512)
  06:00:28 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:02:12 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.286
    nmi_leiden: 0.4088 [OK]
    ari_leiden: 0.1512 [OK]
    silhouette_label: 0.3436 [OK]
    silhouette_batch: 0.6003 [OK]
    isolated_label_asw: 0.4599 [OK]
    graph_connectivity: 0.3065 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9771 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:02:26 Computing scIB metrics: lung / untrained_encoder (d=512)
  06:02:28 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:04:15 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.211
    nmi_leiden: 0.3211 [OK]
    ari_leiden: 0.1262 [OK]
    silhouette_label: 0.3384 [OK]
    silhouette_batch: 0.6043 [OK]
    isolated_label_asw: 0.4608 [OK]
    graph_connectivity: 0.3210 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9676 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:04:36 Computing scIB metrics: lung / bog_pca_512 (d=512)
  06:04:37 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:06:19 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.345
    nmi_leiden: 0.6005 [OK]
    ari_leiden: 0.2892 [OK]
    silhouette_label: 0.3187 [OK]
    silhouette_batch: 0.5658 [OK]
    isolated_label_asw: 0.4587 [OK]
    graph_connectivity: 0.4515 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9848 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:07:48 Computing scIB metrics: lung / geneformer_v2_104m (d=768)
  06:07:49 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:09:35 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.507
    nmi_leiden: 0.6579 [OK]
    ari_leiden: 0.3288 [OK]
    silhouette_label: 0.4188 [OK]
    silhouette_batch: 0.4802 [OK]
    isolated_label_asw: 0.5476 [OK]
    graph_connectivity: 0.6855 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9922 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:10:11 Computing scIB metrics: lung / geneformer_v2_316m (d=1152)
  06:10:13 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD16-negative, CD56-bright natural killer cell, human consists of a    
         single batch or is too small. Skip.                                    
[34mINFO    [0m CD16-positive, CD56-dim natural killer cell, human consists of a single
         batch or is too small. Skip.                                           
[34mINFO    [0m CD4-positive helper T cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m CD8-positive, alpha-beta memory T cell, CD45RO-positive consists of a  
         single batch or is too small. Skip.                                    
[34mINFO    [0m T cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m alpha-beta T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m alveolar type [1;36m1[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m alveolar type [1;36m2[0m fibroblast cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m animal cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m blood vessel endothelial cell consists of a single batch or is too     
         small. Skip.                                                           
[34mINFO    [0m chondrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m ciliated cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m ciliated columnar cell of tracheobronchial tree consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell, human consists of a single batch or is too small. Skip.
[34mINFO    [0m effector CD4-positive, alpha-beta T cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m effector memory CD8-positive, alpha-beta T cell, terminally            
         differentiated consists of a single batch or is too small. Skip.       
[34mINFO    [0m elicited macrophage consists of a single batch or is too small. Skip.  
[34mINFO    [0m epithelial cell of lower respiratory tract consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m goblet cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m intermediate monocyte consists of a single batch or is too small. Skip.
[34mINFO    [0m lung macrophage consists of a single batch or is too small. Skip.      
[34mINFO    [0m lung microvascular endothelial cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m lung neuroendocrine cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m lung pericyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m mature NK T cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mature alpha-beta T cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m mesothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m mesothelial fibroblast consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mucus secreting cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid leukocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m myofibroblast cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m naive B cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m naive thymus-derived CD4-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m naive thymus-derived CD8-positive, alpha-beta T cell consists of a     
         single batch or is too small. Skip.                                    
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m plasmacytoid dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m pulmonary artery endothelial cell consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m pulmonary interstitial fibroblast consists of a single batch or is too 
         small. Skip.                                                           
[34mINFO    [0m squamous epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m stromal cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m tracheobronchial smooth muscle cell consists of a single batch or is   
         too small. Skip.                                                       
[34mINFO    [0m vascular associated smooth muscle cell consists of a single batch or is
         too small. Skip.                                                       
  06:11:57 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.488
    nmi_leiden: 0.6640 [OK]
    ari_leiden: 0.3632 [OK]
    silhouette_label: 0.4497 [OK]
    silhouette_batch: 0.5825 [OK]
    isolated_label_asw: 0.5522 [OK]
    graph_connectivity: 0.7080 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9925 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

============================================================
06:12:45 Processing tissue: liver
06:12:45 Pulling source cells...
  Source: 2000 cells
06:14:17 Pulling target cells...
  Target: 2000 cells
  geneformer: d=512
  scvi: d=50
  scgpt: d=512
  uce: d=1280
  geneformer_v2_104m: loaded from .npy, d=768
  geneformer_v2_316m: loaded from .npy, d=1152
  scprint: .npy not found for liver, skipping
  nicheformer: .npy not found for liver, skipping

06:16:23 Computing scIB metrics: liver / geneformer (d=512)
  06:16:25 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:18:14 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.486
    nmi_leiden: 0.8386 [OK]
    ari_leiden: 0.7722 [OK]
    silhouette_label: 0.5731 [OK]
    silhouette_batch: 0.7588 [OK]
    isolated_label_asw: 0.5415 [OK]
    graph_connectivity: 0.8069 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9994 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:18:21 Computing scIB metrics: liver / scvi (d=50)
  06:18:22 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:19:58 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.337
    nmi_leiden: 0.7112 [OK]
    ari_leiden: 0.5456 [OK]
    silhouette_label: 0.5021 [OK]
    silhouette_batch: 0.6152 [OK]
    isolated_label_asw: 0.5110 [OK]
    graph_connectivity: 0.7249 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9962 [OK]
    ilisi: 0.0143 [OK]
    kbet: N/A [N/A]

06:19:59 Computing scIB metrics: liver / scgpt (d=512)
  06:20:01 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:21:43 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.270
    nmi_leiden: 0.7724 [OK]
    ari_leiden: 0.6557 [OK]
    silhouette_label: 0.5513 [OK]
    silhouette_batch: 0.6625 [OK]
    isolated_label_asw: 0.5314 [OK]
    graph_connectivity: 0.7576 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9990 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:21:48 Computing scIB metrics: liver / uce (d=1280)
  06:21:49 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:23:38 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.371
    nmi_leiden: 0.7586 [OK]
    ari_leiden: 0.5798 [OK]
    silhouette_label: 0.5582 [OK]
    silhouette_batch: 0.6882 [OK]
    isolated_label_asw: 0.5511 [OK]
    graph_connectivity: 0.7175 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9995 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:23:45 Computing scIB metrics: liver / random_projection (d=512)
  06:23:46 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:25:24 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.356
    nmi_leiden: 0.6206 [OK]
    ari_leiden: 0.4817 [OK]
    silhouette_label: 0.4222 [OK]
    silhouette_batch: 0.4518 [OK]
    isolated_label_asw: 0.4465 [OK]
    graph_connectivity: 0.2838 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9839 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:25:29 Computing scIB metrics: liver / untrained_encoder (d=512)
  06:25:31 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:27:07 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.260
    nmi_leiden: 0.5720 [OK]
    ari_leiden: 0.4523 [OK]
    silhouette_label: 0.4165 [OK]
    silhouette_batch: 0.4531 [OK]
    isolated_label_asw: 0.4415 [OK]
    graph_connectivity: 0.3452 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9818 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:27:23 Computing scIB metrics: liver / bog_pca_512 (d=512)
  06:27:25 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:29:02 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.360
    nmi_leiden: 0.7185 [OK]
    ari_leiden: 0.4724 [OK]
    silhouette_label: 0.4205 [OK]
    silhouette_batch: 0.3918 [OK]
    isolated_label_asw: 0.4402 [OK]
    graph_connectivity: 0.5206 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9969 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:29:33 Computing scIB metrics: liver / geneformer_v2_104m (d=768)
  06:29:34 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:31:13 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.520
    nmi_leiden: 0.7487 [OK]
    ari_leiden: 0.5115 [OK]
    silhouette_label: 0.5257 [OK]
    silhouette_batch: 0.4509 [OK]
    isolated_label_asw: 0.5291 [OK]
    graph_connectivity: 0.7365 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9990 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:31:36 Computing scIB metrics: liver / geneformer_v2_316m (d=1152)
  06:31:37 Computing kNN (k=15,50,90)...
[34mINFO    [0m CD1c-positive myeloid dendritic cell consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m CD4-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m Kupffer cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m basophil consists of a single batch or is too small. Skip.             
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m capillary endothelial cell consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m cholangiocyte consists of a single batch or is too small. Skip.        
[34mINFO    [0m classical monocyte consists of a single batch or is too small. Skip.   
[34mINFO    [0m common dendritic progenitor consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m common lymphoid progenitor consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m conventional dendritic cell consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m endothelial cell of lymphatic vessel consists of a single batch or is  
         too small. Skip.                                                       
[34mINFO    [0m epithelial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m erythroblast consists of a single batch or is too small. Skip.         
[34mINFO    [0m erythrocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m erythroid progenitor cell consists of a single batch or is too small.  
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m granulocyte consists of a single batch or is too small. Skip.          
[34mINFO    [0m hematopoietic multipotent progenitor cell consists of a single batch or
         is too small. Skip.                                                    
[34mINFO    [0m hepatic stellate cell consists of a single batch or is too small. Skip.
[34mINFO    [0m intrahepatic cholangiocyte consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m liver dendritic cell consists of a single batch or is too small. Skip. 
[34mINFO    [0m lymphocyte consists of a single batch or is too small. Skip.           
[34mINFO    [0m lymphoid lineage restricted progenitor cell consists of a single batch 
         or is too small. Skip.                                                 
[34mINFO    [0m malignant cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m megakaryocyte-erythroid progenitor cell consists of a single batch or  
         is too small. Skip.                                                    
[34mINFO    [0m myeloid cell consists of a single batch or is too small. Skip.         
[34mINFO    [0m myeloid lineage restricted progenitor cell consists of a single batch  
         or is too small. Skip.                                                 
[34mINFO    [0m neoplastic cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m non-classical monocyte consists of a single batch or is too small.     
         Skip.                                                                  
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m precursor B cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m pro-B cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m proerythroblast consists of a single batch or is too small. Skip.      
[34mINFO    [0m regulatory T cell consists of a single batch or is too small. Skip.    
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m type I pneumocyte consists of a single batch or is too small. Skip.    
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:33:30 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.535
    nmi_leiden: 0.7738 [OK]
    ari_leiden: 0.6467 [OK]
    silhouette_label: 0.5337 [OK]
    silhouette_batch: 0.5509 [OK]
    isolated_label_asw: 0.5392 [OK]
    graph_connectivity: 0.7445 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9993 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

============================================================
06:33:55 Processing tissue: kidney
06:33:55 Pulling source cells...
  Source: 2000 cells
06:34:58 Pulling target cells...
  Target: 370 cells
  geneformer: d=512
  scvi: d=50
  scgpt: d=512
  uce: d=1280
  geneformer_v2_104m: loaded from .npy, d=768
  geneformer_v2_316m: loaded from .npy, d=1152
  scprint: .npy not found for kidney, skipping
  nicheformer: .npy not found for kidney, skipping

06:36:28 Computing scIB metrics: kidney / geneformer (d=512)
  06:36:29 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:37:20 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.487
    nmi_leiden: 0.7634 [OK]
    ari_leiden: 0.6131 [OK]
    silhouette_label: 0.5571 [OK]
    silhouette_batch: 0.7195 [OK]
    isolated_label_asw: 0.5671 [OK]
    graph_connectivity: 0.8223 [OK]
    pcr_comparison: 0.4887 [OK]
    clisi: 0.9948 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:37:23 Computing scIB metrics: kidney / scvi (d=50)
  06:37:24 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:38:04 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.405
    nmi_leiden: 0.6695 [OK]
    ari_leiden: 0.5267 [OK]
    silhouette_label: 0.5402 [OK]
    silhouette_batch: 0.7854 [OK]
    isolated_label_asw: 0.5375 [OK]
    graph_connectivity: 0.8115 [OK]
    pcr_comparison: 0.7045 [OK]
    clisi: 0.9797 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:38:05 Computing scIB metrics: kidney / scgpt (d=512)
  06:38:06 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:38:47 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.348
    nmi_leiden: 0.7051 [OK]
    ari_leiden: 0.4890 [OK]
    silhouette_label: 0.5339 [OK]
    silhouette_batch: 0.4607 [OK]
    isolated_label_asw: 0.5412 [OK]
    graph_connectivity: 0.8030 [OK]
    pcr_comparison: 0.0456 [OK]
    clisi: 0.9898 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:38:48 Computing scIB metrics: kidney / uce (d=1280)
  06:38:49 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:39:38 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.481
    nmi_leiden: 0.7645 [OK]
    ari_leiden: 0.6029 [OK]
    silhouette_label: 0.5646 [OK]
    silhouette_batch: 0.7005 [OK]
    isolated_label_asw: 0.5764 [OK]
    graph_connectivity: 0.7491 [OK]
    pcr_comparison: 0.6316 [OK]
    clisi: 0.9972 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:39:40 Computing scIB metrics: kidney / random_projection (d=512)
  06:39:41 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:40:23 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.447
    nmi_leiden: 0.5420 [OK]
    ari_leiden: 0.4081 [OK]
    silhouette_label: 0.4226 [OK]
    silhouette_batch: 0.6983 [OK]
    isolated_label_asw: 0.4483 [OK]
    graph_connectivity: 0.1784 [OK]
    pcr_comparison: 0.5697 [OK]
    clisi: 0.9321 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:40:25 Computing scIB metrics: kidney / untrained_encoder (d=512)
  06:40:25 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:41:06 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.359
    nmi_leiden: 0.3744 [OK]
    ari_leiden: 0.2344 [OK]
    silhouette_label: 0.4178 [OK]
    silhouette_batch: 0.7517 [OK]
    isolated_label_asw: 0.4436 [OK]
    graph_connectivity: 0.2146 [OK]
    pcr_comparison: 0.1091 [OK]
    clisi: 0.8958 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:41:08 Computing scIB metrics: kidney / bog_pca_512 (d=512)
  06:41:09 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:41:50 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.528
    nmi_leiden: 0.6456 [OK]
    ari_leiden: 0.4729 [OK]
    silhouette_label: 0.4223 [OK]
    silhouette_batch: 0.6643 [OK]
    isolated_label_asw: 0.4571 [OK]
    graph_connectivity: 0.5444 [OK]
    pcr_comparison: 0.4754 [OK]
    clisi: 0.9773 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:41:53 Computing scIB metrics: kidney / geneformer_v2_104m (d=768)
  06:41:54 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:42:35 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.514
    nmi_leiden: 0.7130 [OK]
    ari_leiden: 0.4822 [OK]
    silhouette_label: 0.5427 [OK]
    silhouette_batch: 0.5041 [OK]
    isolated_label_asw: 0.5519 [OK]
    graph_connectivity: 0.7588 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9942 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:42:41 Computing scIB metrics: kidney / geneformer_v2_316m (d=1152)
  06:42:42 Computing kNN (k=15,50,90)...
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of nephron consists of a single batch or is too small. 
         Skip.                                                                  
[34mINFO    [0m epithelial cell of proximal tubule consists of a single batch or is too
         small. Skip.                                                           
[34mINFO    [0m kidney collecting duct intercalated cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney collecting duct principal cell consists of a single batch or is 
         too small. Skip.                                                       
[34mINFO    [0m kidney connecting tubule epithelial cell consists of a single batch or 
         is too small. Skip.                                                    
[34mINFO    [0m kidney distal convoluted tubule epithelial cell consists of a single   
         batch or is too small. Skip.                                           
[34mINFO    [0m kidney interstitial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m kidney loop of Henle thick ascending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin ascending limb epithelial cell consists of a 
         single batch or is too small. Skip.                                    
[34mINFO    [0m kidney loop of Henle thin descending limb epithelial cell consists of a
         single batch or is too small. Skip.                                    
[34mINFO    [0m leukocyte consists of a single batch or is too small. Skip.            
[34mINFO    [0m mesenchymal stem cell consists of a single batch or is too small. Skip.
[34mINFO    [0m native cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m parietal epithelial cell consists of a single batch or is too small.   
         Skip.                                                                  
[34mINFO    [0m podocyte consists of a single batch or is too small. Skip.             
  06:43:24 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.534
    nmi_leiden: 0.7692 [OK]
    ari_leiden: 0.5988 [OK]
    silhouette_label: 0.5553 [OK]
    silhouette_batch: 0.5967 [OK]
    isolated_label_asw: 0.5600 [OK]
    graph_connectivity: 0.8272 [OK]
    pcr_comparison: 0.1140 [OK]
    clisi: 0.9959 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

============================================================
06:43:32 Processing tissue: brain
06:43:32 Pulling source cells...
  Source: 2000 cells
06:44:43 Pulling target cells...
  Target: 59 cells
  geneformer: d=512
  scvi: d=50
  scgpt: d=512
  uce: d=1280
  geneformer_v2_104m: loaded from .npy, d=768
  geneformer_v2_316m: loaded from .npy, d=1152
  scprint: .npy not found for brain, skipping
  nicheformer: .npy not found for brain, skipping

06:46:10 Computing scIB metrics: brain / geneformer (d=512)
  06:46:11 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:46:51 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.413
    nmi_leiden: 0.5521 [OK]
    ari_leiden: 0.3212 [OK]
    silhouette_label: 0.5282 [OK]
    silhouette_batch: 0.7917 [OK]
    isolated_label_asw: 0.5377 [OK]
    graph_connectivity: 0.8014 [OK]
    pcr_comparison: 0.8956 [OK]
    clisi: 0.9807 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:46:56 Computing scIB metrics: brain / scvi (d=50)
  06:46:57 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:47:29 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.451
    nmi_leiden: 0.5965 [OK]
    ari_leiden: 0.4119 [OK]
    silhouette_label: 0.4784 [OK]
    silhouette_batch: 0.4953 [OK]
    isolated_label_asw: 0.5370 [OK]
    graph_connectivity: 0.6921 [OK]
    pcr_comparison: 0.7193 [OK]
    clisi: 0.9771 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:47:30 Computing scIB metrics: brain / scgpt (d=512)
  06:47:30 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:48:06 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.354
    nmi_leiden: 0.5205 [OK]
    ari_leiden: 0.3385 [OK]
    silhouette_label: 0.4545 [OK]
    silhouette_batch: 0.7591 [OK]
    isolated_label_asw: 0.5314 [OK]
    graph_connectivity: 0.7723 [OK]
    pcr_comparison: 0.8919 [OK]
    clisi: 0.9810 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:48:07 Computing scIB metrics: brain / uce (d=1280)
  06:48:08 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:48:45 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.412
    nmi_leiden: 0.5206 [OK]
    ari_leiden: 0.3407 [OK]
    silhouette_label: 0.5234 [OK]
    silhouette_batch: 0.7714 [OK]
    isolated_label_asw: 0.5542 [OK]
    graph_connectivity: 0.6609 [OK]
    pcr_comparison: 0.8872 [OK]
    clisi: 0.9822 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:48:47 Computing scIB metrics: brain / random_projection (d=512)
  06:48:48 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:49:21 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.369
    nmi_leiden: 0.3842 [OK]
    ari_leiden: 0.1514 [OK]
    silhouette_label: 0.3708 [OK]
    silhouette_batch: 0.2583 [OK]
    isolated_label_asw: 0.4277 [OK]
    graph_connectivity: 0.2699 [OK]
    pcr_comparison: 0.1151 [OK]
    clisi: 0.9715 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:49:27 Computing scIB metrics: brain / untrained_encoder (d=512)
  06:49:28 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:50:02 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.333
    nmi_leiden: 0.3499 [OK]
    ari_leiden: 0.1586 [OK]
    silhouette_label: 0.3581 [OK]
    silhouette_batch: 0.2672 [OK]
    isolated_label_asw: 0.4325 [OK]
    graph_connectivity: 0.3408 [OK]
    pcr_comparison: 0.0000 [OK]
    clisi: 0.9596 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:50:05 Computing scIB metrics: brain / bog_pca_512 (d=512)
  06:50:05 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:50:39 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.472
    nmi_leiden: 0.4867 [OK]
    ari_leiden: 0.2806 [OK]
    silhouette_label: 0.3204 [OK]
    silhouette_batch: 0.2202 [OK]
    isolated_label_asw: 0.4217 [OK]
    graph_connectivity: 0.4060 [OK]
    pcr_comparison: 0.0293 [OK]
    clisi: 0.9781 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:50:50 Computing scIB metrics: brain / geneformer_v2_104m (d=768)
  06:50:50 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:51:25 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.478
    nmi_leiden: 0.5119 [OK]
    ari_leiden: 0.2206 [OK]
    silhouette_label: 0.4474 [OK]
    silhouette_batch: 0.4976 [OK]
    isolated_label_asw: 0.5224 [OK]
    graph_connectivity: 0.7631 [OK]
    pcr_comparison: 0.5032 [OK]
    clisi: 0.9816 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

06:51:32 Computing scIB metrics: brain / geneformer_v2_316m (d=1152)
  06:51:32 Computing kNN (k=15,50,90)...
[34mINFO    [0m B cell consists of a single batch or is too small. Skip.               
[34mINFO    [0m CD8-positive, alpha-beta T cell consists of a single batch or is too   
         small. Skip.                                                           
[34mINFO    [0m bronchus fibroblast of lung consists of a single batch or is too small.
         Skip.                                                                  
[34mINFO    [0m dendritic cell consists of a single batch or is too small. Skip.       
[34mINFO    [0m endothelial cell consists of a single batch or is too small. Skip.     
[34mINFO    [0m epithelial cell of lung consists of a single batch or is too small.    
         Skip.                                                                  
[34mINFO    [0m fibroblast of lung consists of a single batch or is too small. Skip.   
[34mINFO    [0m mast cell consists of a single batch or is too small. Skip.            
[34mINFO    [0m mature T cell consists of a single batch or is too small. Skip.        
[34mINFO    [0m microglial cell consists of a single batch or is too small. Skip.      
[34mINFO    [0m monocyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m mural cell consists of a single batch or is too small. Skip.           
[34mINFO    [0m natural killer cell consists of a single batch or is too small. Skip.  
[34mINFO    [0m neuron consists of a single batch or is too small. Skip.               
[34mINFO    [0m neutrophil consists of a single batch or is too small. Skip.           
[34mINFO    [0m oligodendrocyte consists of a single batch or is too small. Skip.      
[34mINFO    [0m oligodendrocyte precursor cell consists of a single batch or is too    
         small. Skip.                                                           
[34mINFO    [0m pericyte consists of a single batch or is too small. Skip.             
[34mINFO    [0m plasma cell consists of a single batch or is too small. Skip.          
[34mINFO    [0m smooth muscle cell consists of a single batch or is too small. Skip.   
[34mINFO    [0m vein endothelial cell consists of a single batch or is too small. Skip.
  06:52:11 WARNING: kBET failed: 'numpy.float64' object has no attribute 'values'
  Cell-type recovery F1: 0.479
    nmi_leiden: 0.5459 [OK]
    ari_leiden: 0.4035 [OK]
    silhouette_label: 0.4774 [OK]
    silhouette_batch: 0.5775 [OK]
    isolated_label_asw: 0.5332 [OK]
    graph_connectivity: 0.7587 [OK]
    pcr_comparison: 0.6636 [OK]
    clisi: 0.9823 [OK]
    ilisi: 0.0000 [OK]
    kbet: N/A [N/A]

============================================================
06:52:20 All scores collected. Running construct-validity tests...

----------------------------------------
06:52:20 Testing metric: nmi_leiden (class: bio)
  T1: PASS | delta=0.2295 CI=[0.1448, 0.3091]
  T2: deferred (requires multi-d re-embedding)
  T3-bio: PASS | rho=0.416, p=0.0143, n=36

----------------------------------------
06:52:27 Testing metric: ari_leiden (class: bio)
  T1: PASS | delta=0.1936 CI=[0.0793, 0.3023]
  T2: deferred (requires multi-d re-embedding)
  T3-bio: PASS | rho=0.378, p=0.0239, n=36

----------------------------------------
06:52:33 Testing metric: silhouette_label (class: bio)
  T1: PASS | delta=0.1213 CI=[0.0915, 0.1514]
  T2: deferred (requires multi-d re-embedding)
  T3-bio: PASS | rho=0.431, p=0.0104, n=36

----------------------------------------
06:52:39 Testing metric: clisi (class: bio)
  T1: PASS | delta=0.0321 CI=[0.0146, 0.0540]
  T2: deferred (requires multi-d re-embedding)
  T3-bio: PASS (underpowered) | rho=0.310, p=0.0685, n=36

----------------------------------------
06:52:46 Testing metric: isolated_label_asw (class: bio)
  T1: PASS | delta=0.0956 CI=[0.0859, 0.1056]
  T2: deferred (requires multi-d re-embedding)
  T3-bio: PASS | rho=0.477, p=0.0049, n=36

----------------------------------------
06:52:52 Testing metric: silhouette_batch (class: batch)
  T1: PASS | delta=0.1302 CI=[0.0075, 0.2607]
  T2: deferred (requires multi-d re-embedding)
  T3-batch: deferred (requires synthetic batch injection)

----------------------------------------
06:52:52 Testing metric: ilisi (class: batch)
  T1: PASS | delta=0.0062 CI=[0.0001, 0.0172]
  T2: deferred (requires multi-d re-embedding)
  T3-batch: deferred (requires synthetic batch injection)

----------------------------------------
06:52:52 Testing metric: kbet (class: batch)
  T1: N/A (insufficient data)
  T2: deferred (requires multi-d re-embedding)
  T3-batch: deferred (requires synthetic batch injection)

----------------------------------------
06:52:52 Testing metric: graph_connectivity (class: batch)
  T1: PASS | delta=0.4708 CI=[0.4309, 0.5146]
  T2: deferred (requires multi-d re-embedding)
  T3-batch: deferred (requires synthetic batch injection)

----------------------------------------
06:52:53 Testing metric: pcr_comparison (class: batch)
  T1: FAIL (CI includes zero) | delta=0.1735 CI=[-0.0257, 0.3584]
  T2: deferred (requires multi-d re-embedding)
  T3-batch: deferred (requires synthetic batch injection)

06:52:53 Summary saved to results/exp10_scib_audit/summary_20260724_054631.json

============================================================
06:52:53 SCORECARD
Metric                    Class    T1                        T2              T3                       
----------------------------------------------------------------------------------------------------
nmi_leiden                bio      PASS                      N/A             PASS                     
ari_leiden                bio      PASS                      N/A             PASS                     
silhouette_label          bio      PASS                      N/A             PASS                     
clisi                     bio      PASS                      N/A             PASS (underpowered)      
isolated_label_asw        bio      PASS                      N/A             PASS                     
silhouette_batch          batch    PASS                      N/A             deferred                 
ilisi                     batch    PASS                      N/A             deferred                 
kbet                      batch    N/A                       N/A             deferred                 
graph_connectivity        batch    PASS                      N/A             deferred                 
pcr_comparison            batch    FAIL (CI includes zero)   N/A             deferred                 

HD (headline): 5/10 metrics pass T1+T3
(T2 deferred to expanded panel with multi-d re-embedding)


=== STDERR ===

Tissues:   0%|          | 0/4 [00:00<?, ?it/s]/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)


  Embeddings (lung):   0%|          | 0/9 [00:00<?, ?it/s][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/pynndescent/pynndescent_.py:939: UserWarning: Failed to correctly find n_neighbors for some samples. Results may be less than ideal. Try re-running with different parameters.
  warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  11%|█         | 1/9 [03:07<24:59, 187.43s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  22%|██▏       | 2/9 [04:55<16:26, 140.98s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  33%|███▎      | 3/9 [06:46<12:42, 127.08s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/pynndescent/pynndescent_.py:939: UserWarning: Failed to correctly find n_neighbors for some samples. Results may be less than ideal. Try re-running with different parameters.
  warn(


  Embeddings (lung):  44%|████▍     | 4/9 [08:50<10:29, 125.83s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/pynndescent/pynndescent_.py:939: UserWarning: Failed to correctly find n_neighbors for some samples. Results may be less than ideal. Try re-running with different parameters.
  warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  56%|█████▌    | 5/9 [10:50<08:14, 123.64s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  67%|██████▋   | 6/9 [12:59<06:17, 125.69s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/pynndescent/pynndescent_.py:939: UserWarning: Failed to correctly find n_neighbors for some samples. Results may be less than ideal. Try re-running with different parameters.
  warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/sklearn/linear_model/_logistic.py:465: ConvergenceWarning: lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
  n_iter_i = _check_optimize_result(
/usr/local/lib/python3.11/site-packages/sklearn/linear_model/_logistic.py:465: ConvergenceWarning: lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
  n_iter_i = _check_optimize_result(
/usr/local/lib/python3.11/site-packages/sklearn/linear_model/_logistic.py:465: ConvergenceWarning: lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
  n_iter_i = _check_optimize_result(
/usr/local/lib/python3.11/site-packages/sklearn/linear_model/_logistic.py:465: ConvergenceWarning: lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
  n_iter_i = _check_optimize_result(
/usr/local/lib/python3.11/site-packages/sklearn/linear_model/_logistic.py:465: ConvergenceWarning: lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
  n_iter_i = _check_optimize_result(


  Embeddings (lung):  78%|███████▊  | 7/9 [16:11<04:54, 147.34s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung):  89%|████████▉ | 8/9 [18:35<02:26, 146.13s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (lung): 100%|██████████| 9/9 [21:09<00:00, 148.54s/it][A

                                                                   [A
Tissues:  25%|██▌       | 1/4 [26:07<1:18:21, 1567.31s/it]/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)


  Embeddings (liver):   0%|          | 0/9 [00:00<?, ?it/s][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  11%|█         | 1/9 [01:57<15:37, 117.18s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  22%|██▏       | 2/9 [03:35<12:24, 106.37s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  33%|███▎      | 3/9 [05:24<10:43, 107.20s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  44%|████▍     | 4/9 [07:21<09:15, 111.14s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  56%|█████▌    | 5/9 [09:05<07:15, 108.80s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  67%|██████▋   | 6/9 [10:59<05:31, 110.52s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  78%|███████▊  | 7/9 [13:09<03:53, 116.80s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver):  89%|████████▉ | 8/9 [15:12<01:58, 118.75s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (liver): 100%|██████████| 9/9 [17:31<00:00, 125.08s/it][A

                                                                    [A
Tissues:  50%|█████     | 2/4 [47:17<46:24, 1392.28s/it]  /usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)


  Embeddings (kidney):   0%|          | 0/9 [00:00<?, ?it/s][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  11%|█         | 1/9 [00:55<07:20, 55.03s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  22%|██▏       | 2/9 [01:36<05:29, 47.12s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  33%|███▎      | 3/9 [02:19<04:32, 45.34s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  44%|████▍     | 4/9 [03:11<03:59, 47.87s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  56%|█████▌    | 5/9 [03:56<03:06, 46.71s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  67%|██████▋   | 6/9 [04:40<02:17, 45.71s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  78%|███████▊  | 7/9 [05:24<01:30, 45.36s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney):  89%|████████▉ | 8/9 [06:12<00:46, 46.19s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (kidney): 100%|██████████| 9/9 [07:03<00:00, 47.79s/it][A

                                                                    [A
Tissues:  75%|███████▌  | 3/4 [56:54<17:00, 1020.18s/it]/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)


  Embeddings (brain):   0%|          | 0/9 [00:00<?, ?it/s][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (brain):  11%|█         | 1/9 [00:46<06:10, 46.30s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)


  Embeddings (brain):  22%|██▏       | 2/9 [01:19<04:31, 38.75s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)


  Embeddings (brain):  33%|███▎      | 3/9 [01:56<03:48, 38.02s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (brain):  44%|████▍     | 4/9 [02:36<03:14, 38.82s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)


  Embeddings (brain):  56%|█████▌    | 5/9 [03:17<02:37, 39.32s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_pcr_comparison.py:49: UserWarning: PCR comparison score is negative, meaning variance contribution increased after integration. Setting to 0.
  warnings.warn(


  Embeddings (brain):  67%|██████▋   | 6/9 [03:54<01:56, 38.75s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)


  Embeddings (brain):  78%|███████▊  | 7/9 [04:39<01:21, 40.82s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)


  Embeddings (brain):  89%|████████▉ | 8/9 [05:21<00:41, 41.16s/it][A/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
/usr/local/lib/python3.11/site-packages/scib_metrics/_graph_connectivity.py:30: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  tab = pd.value_counts(comps)
/usr/local/lib/python3.11/site-packages/scib_metrics/_kbet.py:181: FutureWarning: pandas.value_counts is deprecated and will be removed in a future version. Use pd.Series(obj).value_counts() instead.
  comp_size = pd.value_counts(labs)


  Embeddings (brain): 100%|██████████| 9/9 [06:10<00:00, 43.45s/it][A

                                                                   [A
Tissues: 100%|██████████| 4/4 [1:05:42<00:00, 825.82s/it]
Tissues: 100%|██████████| 4/4 [1:05:42<00:00, 985.58s/it]


=== RETURN CODE: 0 ===
