══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP406
📁 Output directory: data/SP406/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,368 cells × 1,936 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 9 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 9 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 19299 unique values
      - doublet_scores: 441 unique values
      - n_genes: 4337 unique values
      - predicted_doublets: 1 unique values

⚠️  cellinfo.csv not found at: table/cellinfo.csv
   Will use raw cell type names without mapping

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []
==========================================
Job finished at: Sun Feb 15 12:59:20 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 01:00:11 AM CST 2026
Running on node: biohpc007
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP406
📁 Output directory: data/SP406/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,368 cells × 1,936 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 9 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 9 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 19299 unique values
      - doublet_scores: 441 unique values
      - n_genes: 4337 unique values
      - predicted_doublets: 1 unique values

⚠️  cellinfo.csv not found at: table/cellinfo.csv
   Will use raw cell type names without mapping

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []
==========================================
Job finished at: Sun Feb 15 01:00:17 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 01:00:56 AM CST 2026
Running on node: biohpc007
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP406
📁 Output directory: data/SP406/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,368 cells × 1,936 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 9 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 9 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 19299 unique values
      - doublet_scores: 441 unique values
      - n_genes: 4337 unique values
      - predicted_doublets: 1 unique values

⚠️  cellinfo.csv not found at: table/cellinfo.csv
   Will use raw cell type names without mapping

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []
==========================================
Job finished at: Sun Feb 15 01:01:01 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 01:05:29 AM CST 2026
Running on node: biohpc007
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP406
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP406/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,368 cells × 1,936 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 9 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 9 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 19299 unique values
      - doublet_scores: 441 unique values
      - n_genes: 4337 unique values
      - predicted_doublets: 1 unique values

⚠️  cellinfo.csv not found at: table/cellinfo.csv
   Will use raw cell type names without mapping

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []
==========================================
Job finished at: Sun Feb 15 01:05:34 AM CST 2026
==========================================
============================================================
📂 文件: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
============================================================

🔢 维度: 22368 cells × 0 genes

📋 obs 列 (9):
   - CellType (category)
   - DevoStage (category)
   - Org_celltype (category)
   - Region (category)
   - Tissue (category)
   - _index (object)
   - doublet_scores (float64)
   - n_genes (int64)
   - predicted_doublets (object)

🧬 var 列 (0):

============================================================
📊 分类列统计:
============================================================

  【CellType】(9 类):
      Neu: 9907
      Ex: 5828
      Others: 2243
      In: 2057
      Mic: 748
      OPC: 613
      Epend: 548
      Olg: 291
      End: 133

  【DevoStage】(1 类):
      Adult: 22368

  【Org_celltype】(9 类):
      Neu: 9907
      Ex: 5828
      Others: 2243
      In: 2057
      Mic: 748
      OPC: 613
      Epend: 548
      Olg: 291
      End: 133

  【Region】(1 类):
      Telencephalon: 22368

  【Tissue】(1 类):
      Brain: 22368

  【_index】(19299 类):
      Carassius_auratus_37910612_2023_Rank0001_1723: 2
      Carassius_auratus_37910612_2023_Rank0001_19289: 2
      Carassius_auratus_37910612_2023_Rank0001_19334: 2
      Carassius_auratus_37910612_2023_Rank0001_34154: 2
      Carassius_auratus_37910612_2023_Rank0001_33482: 2
      Carassius_auratus_37910612_2023_Rank0001_33518: 2
      Carassius_auratus_37910612_2023_Rank0001_34167: 2
      Carassius_auratus_37910612_2023_Rank0001_34257: 2
      Carassius_auratus_37910612_2023_Rank0001_33376: 2
      Carassius_auratus_37910612_2023_Rank0001_34242: 2
      ... 共 19299 类，仅显示前 10

  【predicted_doublets】(1 类):
      : 22368
============================================================
📂 文件: /mnt/alamo01/projects/test_20241129/LCA/SP451/SP451.h5ad
============================================================

🔢 维度: 275033 cells × 16999 genes

📋 obs 列 (16):
   - Org_celltype (category)
   - Tissue (category)
   - n_genes (int64)
   - FolderID (category)
   - LatinName (category)
   - celltypist_predicted_labels (category)
   - celltypist_over_clustering (int64)
   - celltypist_majority_voting (category)
   - leiden_res1.0 (category)
   - deepseek_v3.2_celltype (category)
   - deepseek_v3.2_confidence (category)
   - deepseek_v3.2_Ann_Label_Standardized (category)
   - deepseek_v3.2_check_is_correct (category)
   - deepseek_v3.2_check_suggestion (category)
   - deepseek_v3.2_check_contamination (category)
   - laca_curated_celltype_v3 (category)

🧬 var 列 (0):

📐 obsm (降维):
   - X_pca: (275033, 50)
   - X_umap: (275033, 2)

📦 uns: ['FolderID_colors', 'LatinName_colors', 'Org_celltype_colors', 'Tissue_colors', 'neighbors', 'pca', 'umap']

📚 layers: ['counts']

============================================================
📊 分类列统计:
============================================================

  【Org_celltype】(84 类):
      Endothelial cell: 38570
      Acinar cell: 30795
      Fibroblast: 24379
      Proximal tubule cell: 21294
      T cell: 14132
      Principal cell: 13420
      Granule cell: 12179
      Melanotrope cell: 11305
      Microglia: 10585
      Smooth muscle cell: 9740
      ... 共 84 类，仅显示前 10

  【Tissue】(20 类):
      Kidney: 43236
      Pancreas: 37908
      Pituitary gland: 23598
      Muscle: 21004
      Cerebellum: 16017
      Ovary: 15855
      Pineal gland: 14404
      Epididymis: 11694
      Liver: 10588
      Testis: 9925
      ... 共 20 类，仅显示前 10

  【FolderID】(20 类):
      Equus_asinus_40013957_2025_Rank005: 43236
      Equus_asinus_40013957_2025_Rank011: 37908
      Equus_asinus_40013957_2025_Rank014: 23598
      Equus_asinus_40013957_2025_Rank009: 21004
      Equus_asinus_40013957_2025_Rank001: 16017
      Equus_asinus_40013957_2025_Rank010: 15855
      Equus_asinus_40013957_2025_Rank013: 14404
      Equus_asinus_40013957_2025_Rank003: 11694
      Equus_asinus_40013957_2025_Rank007: 10588
      Equus_asinus_40013957_2025_Rank019: 9925
      ... 共 20 类，仅显示前 10

  【LatinName】(1 类):
      Equus asinus: 275033

  【celltypist_predicted_labels】(62 类):
      Pancreas ductal cells: 37029
      Endothelial cells: 34979
      Proximal tubule cells: 28833
      Stromal cells: 23897
      Inhibitory neurons: 14729
      Microglia: 12587
      T_NKT cells: 9006
      Peritubular myoid cells: 8794
      Monocytes: 8468
      Smooth muscle cells: 6723
      ... 共 62 类，仅显示前 10

  【celltypist_majority_voting】(48 类):
      Endothelial cells: 37916
      Pancreas ductal cells: 37392
      Proximal tubule cells: 31244
      Stromal cells: 21082
      Inhibitory neurons: 15628
      Microglia: 13408
      Corticotropes: 11164
      T_NKT cells: 9362
      Peritubular myoid cells: 9224
      Monocytes: 9208
      ... 共 48 类，仅显示前 10

  【leiden_res1.0】(454 类):
      Pancreas_CC07: 6369
      Pituitary gland_CC08: 5809
      Kidney_CC05: 4932
      Pancreas_CC08: 4815
      Kidney_CC02: 4696
      Kidney_CC03: 4554
      Pineal gland_CC07: 4493
      Pancreas_CC14: 4327
      Kidney_CC16: 4299
      Pancreas_CC01: 4218
      ... 共 454 类，仅显示前 10

  【deepseek_v3.2_celltype】(111 类):
      Endothelial cells: 33486
      Acinar cells: 27227
      Proximal tubule cells: 24561
      Contamination: T cells: 19678
      Fibroblasts: 15501
      Stromal cells: 13180
      Granule cells: 11889
      Contamination: Neuronal cells: 9212
      Microglia: 9032
      T cells: 8122
      ... 共 111 类，仅显示前 10

  【deepseek_v3.2_confidence】(3 类):
      High: 272284
      Medium: 2649
      Low: 100

  【deepseek_v3.2_Ann_Label_Standardized】(78 类):
      Endothelial cells: 35031
      T cells: 27800
      Acinar cells: 27227
      Proximal tubule cells: 24561
      Neuronal cells: 15613
      Fibroblasts: 15537
      Stromal cells: 13180
      Granule cells: 11889
      Microglia: 9683
      Plasma B cells: 8467
      ... 共 78 类，仅显示前 10

  【deepseek_v3.2_check_is_correct】(2 类):
      True: 145555
      False: 129478

  【deepseek_v3.2_check_suggestion】(87 类):
      Endothelial cells: 35951
      Proximal tubule cells: 25472
      Acinar cells: 22844
      Stromal cells: 19618
      Contamination: T cells: 18683
      Inhibitory neurons: 12236
      Microglia: 10526
      Contamination: Neurons: 9984
      Fibroblasts: 9638
      Pancreas ductal cells: 8443
      ... 共 87 类，仅显示前 10

  【deepseek_v3.2_check_contamination】(2 类):
      False: 220398
      True: 54635

  【laca_curated_celltype_v3】(72 类):
      Endothelial cells: 35951
      Proximal tubule cells: 25472
      T cells: 25425
      Acinar cells: 22844
      Stromal cells: 19618
      Inhibitory neurons: 12236
      Microglia: 10526
      Neurons: 9984
      Fibroblasts: 9638
      Pancreas ductal cells: 8443
      ... 共 72 类，仅显示前 10
==========================================
Job started at: Sun Feb 15 02:35:06 AM CST 2026
Running on node: biohpc004
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP451
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP451/SP451.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 275,033 cells × 16,999 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 84 unique values
      - Tissue: 20 unique values
      - n_genes: 3810 unique values
      - FolderID: 20 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 62 unique values
      - celltypist_over_clustering: 411 unique values
      - celltypist_majority_voting: 48 unique values
      - leiden_res1.0: 454 unique values
      - deepseek_v3.2_celltype: 111 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
==========================================
Job finished at: Sun Feb 15 02:35:26 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 02:38:33 AM CST 2026
Running on node: biohpc004
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP451
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP451/SP451.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 275,033 cells × 16,999 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 84 unique values
      - Tissue: 20 unique values
      - n_genes: 3810 unique values
      - FolderID: 20 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 62 unique values
      - celltypist_over_clustering: 411 unique values
      - celltypist_majority_voting: 48 unique values
      - leiden_res1.0: 454 unique values
      - deepseek_v3.2_celltype: 111 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
==========================================
Job finished at: Sun Feb 15 02:38:53 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 02:43:00 AM CST 2026
Running on node: biohpc004
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP451
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP451/SP451.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 275,033 cells × 16,999 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 84 unique values
      - Tissue: 20 unique values
      - n_genes: 3810 unique values
      - FolderID: 20 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 62 unique values
      - celltypist_over_clustering: 411 unique values
      - celltypist_majority_voting: 48 unique values
      - leiden_res1.0: 454 unique values
      - deepseek_v3.2_celltype: 111 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (275033, 2)
   X range: [-8.80, 24.33]
   Y range: [-13.03, 23.83]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 72
   Mapped unique types: 72

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             18     37,718
   Immune cells             16     75,104
   Epithelial cells         23     83,935
   Stromal cells             6     34,550
   Muscle cells              3      4,144
   Germ cells                2        706
   Endothelial cells         1     35,951
   Other                     3      2,925
   Other                     3      2,925
   ────────────────────────────────────────
   TOTAL                    72    275,033

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/umap.bin.gz (gzip compressed)...
   ✅ 275,033 cells × 10 bytes
   📦 Uncompressed: 2.62 MB
   📦 Compressed:   2.10 MB (19.9% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/umap_meta.json ...
   ✅ 11.6 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/celltype_legend.json ...
   ✅ 14.0 KB

🔍 Verification (first 3 cells):
   Cell 0: (   18.75,     8.87) idx=  5 "Inhibitory neurons" ✅
   Cell 1: (   19.73,    12.51) idx=  5 "Inhibitory neurons" ✅
   Cell 2: (   21.26,    13.27) idx= 25 "Microglia" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 20 tissues
      - Kidney: 43,236 cells
      - Pancreas: 37,908 cells
      - Pituitary gland: 23,598 cells
      - Muscle: 21,004 cells
      - Cerebellum: 16,017 cells
      ... and 15 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP451/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 275,033 cells × 16,999 genes

💾 gene_list.json: 16,999 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,999 genes

   📊 Summary:
      gene_list.json   : 155.4 KB
      genes/*.bin.gz   : 1 files, 63.5 KB total
      Uncompressed     : ~1074.3 KB
      Compression      : 94.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

📄 Generated files:
   SP451/
   ├── umap.bin.gz           (2.10 MB)
   ├── umap_meta.json        (11.6 KB)
   ├── celltype_legend.json  (14.0 KB)
   ├── tissue_info.json      (1.2 KB)
   ├── config.json
   ├── gene_list.json        (155.4 KB, 16,999 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP451
   • Total cells:         275,033
   • Cell types:               72
   • Genes (total):        16,999
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,999 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP451

==========================================
Job finished at: Sun Feb 15 02:43:21 AM CST 2026
==========================================
============================================================
📂 文件: /mnt/alamo01/projects/test_20241129/LCA/SP020/SP020.h5ad
============================================================

🔢 维度: 799880 cells × 17305 genes

📋 obs 列 (38):
   - SampleID (category)
   - SpecieID (category)
   - RegionID (category)
   - Double_score (float64)
   - Double_result (category)
   - n_genes_by_counts (int32)
   - total_counts (int64)
   - total_counts_mt (int64)
   - pct_counts_mt (float64)
   - n_genes (int64)
   - Org_celltype (category)
   - FolderID (category)
   - LatinName (category)
   - Specie (category)
   - Tissue (category)
   - CommonName (category)
   - SPID (category)
   - SPRank (category)
   - TissueT1 (category)
   - TissueT2 (category)
   - TissueT3 (category)
   - TissueID (category)
   - SystemID (category)
   - System (category)
   - Celltype_Source (category)
   - Celltype (category)
   - Celltype_Abbreviation (category)
   - CelltypeID (category)
   - MajorCelltype (category)
   - MajorCelltypeID (category)
   - leiden_res2.0 (category)
   - deepseek_v3.2_celltype (category)
   - deepseek_v3.2_confidence (category)
   - deepseek_v3.2_Ann_Label_Standardized (category)
   - deepseek_v3.2_check_is_correct (category)
   - deepseek_v3.2_check_suggestion (category)
   - deepseek_v3.2_check_contamination (category)
   - laca_curated_celltype_v3 (category)

🧬 var 列 (0):

📐 obsm (降维):
   - X_pca: (799880, 50)
   - X_umap: (799880, 2)

📦 uns: ['FolderID_colors', 'LatinName_colors', 'Org_celltype_colors', 'SpecieID_colors', 'Tissue_colors', 'neighbors', 'pca', 'umap']

📚 layers: ['counts']

============================================================
📊 分类列统计:
============================================================

  【SampleID】(95 类):
      A03T19R02S01: 21467
      A03T04R05S01: 14235
      A03T46R01S01: 14034
      A03T04R03S01: 12308
      A02T01R01S01: 12235
      A03T54R01S01: 11646
      A03T53R01S01: 11302
      A03T32R01S01: 11180
      A02T27R01S01: 11083
      A03T50R01S01: 10798
      ... 共 95 类，仅显示前 10

  【SpecieID】(2 类):
      A03: 429610
      A02: 370270

  【RegionID】(49 类):
      T19R02: 29264
      T46R01: 23731
      T01R01: 22545
      T04R05: 21737
      T54R01: 21173
      T48R01: 20432
      T04R01: 20072
      T33R01: 19896
      T04R03: 19708
      T53R01: 19430
      ... 共 49 类，仅显示前 10

  【Double_result】(1 类):
      Singlet: 799880

  【Org_celltype】(1 类):
      Unknown: 799880

  【FolderID】(95 类):
      A03T19R02S01: 21467
      A03T04R05S01: 14235
      A03T46R01S01: 14034
      A03T04R03S01: 12308
      A02T01R01S01: 12235
      A03T54R01S01: 11646
      A03T53R01S01: 11302
      A03T32R01S01: 11180
      A02T27R01S01: 11083
      A03T50R01S01: 10798
      ... 共 95 类，仅显示前 10

  【LatinName】(1 类):
      Macaca mulatta: 799880

  【Specie】(1 类):
      Macaca mulatta: 799880

  【Tissue】(38 类):
      Neocortex: 77748
      Colon: 72748
      Stomach: 39716
      Spleen: 35195
      Cartilage: 31202
      Pituitary gland: 23731
      Salivary gland: 22545
      Hypothalamus: 21173
      Striatum: 20432
      Skeletal muscle: 19896
      ... 共 38 类，仅显示前 10

  【CommonName】(1 类):
      Rhesus macaque: 799880

  【SPID】(1 类):
      SP020: 799880

  【SPRank】(1 类):
      9.0: 799880

  【TissueT1】(30 类):
      Brain: 190465
      Intestine: 100648
      Stomach: 39716
      Spleen: 35195
      Cartilage: 31202
      Salivary gland: 22545
      Muscle: 19896
      Pancreas: 19406
      Blood: 19147
      Adrenal gland: 18950
      ... 共 30 类，仅显示前 10

  【TissueT2】(37 类):
      Large intestine: 87639
      Neocortex: 77748
      Stomach: 39716
      Spleen: 35195
      Cartilage: 31202
      Pituitary gland: 23731
      Salivary gland: 22545
      Hypothalamus: 21173
      Striatum: 20432
      Skeletal muscle: 19896
      ... 共 37 类，仅显示前 10

  【TissueT3】(40 类):
      Colon: 87639
      Stomach: 39716
      Spleen: 35195
      Cartilage: 31202
      Pituitary gland: 23731
      Salivary gland: 22545
      Parietal lobe: 21737
      Hypothalamus: 21173
      Striatum: 20432
      Temporal lobe: 20072
      ... 共 40 类，仅显示前 10

  【TissueID】(40 类):
      sys05tis07: 87639
      sys05tis03: 39716
      sys02tis04: 35195
      sys08tis02: 31202
      sys07tis01: 23731
      sys05tis08: 22545
      sys01tis03: 21737
      sys01tis07: 21173
      sys01tis08: 20432
      sys01tis04: 20072
      ... 共 40 类，仅显示前 10

  【SystemID】(10 类):
      sys05: 233155
      sys01: 216892
      sys02: 86690
      sys07: 79852
      sys08: 69805
      sys03: 33249
      sys09: 26657
      sys06: 24998
      sys10: 14675
      sys04: 13907

  【System】(10 类):
      Digestive system: 233155
      Nervous system: 216892
      Immune system: 86690
      Endocrine system: 79852
      Motor system: 69805
      Cardiovascular system: 33249
      Urinary system: 26657
      Reproductive system: 24998
      Sensory system: 14675
      Respiratory system: 13907

  【Celltype_Source】(1 类):
      annotation: 799880

  【Celltype】(110 类):
      Oligodendrocytes: 71282
      T_NKT cells: 55969
      Stromal cells: 53214
      Enterocytes: 52860
      B cells: 48092
      Excitatory neurons: 44745
      Inhibitory neurons: 32881
      Endothelial cells: 32314
      Type II myonuclei: 28947
      Monocytes: 28583
      ... 共 110 类，仅显示前 10

  【Celltype_Abbreviation】(110 类):
      Oligo: 71282
      T_NKT: 55969
      Stromal: 53214
      Entero: 52860
      B: 48092
      EX: 44745
      IN: 32881
      Endo: 32314
      Myonuc_II: 28947
      Mono: 28583
      ... 共 110 类，仅显示前 10

  【CelltypeID】(110 类):
      Major001CT019A: 71282
      Major002CT022B: 55969
      Major004CT026A: 53214
      Major003CT022A: 52860
      Major002CT001A: 48092
      Major001CT009A: 44745
      Major001CT014A: 32881
      Major007CT001A: 32314
      Major005CT008A: 28947
      Major002CT016A: 28583
      ... 共 110 类，仅显示前 10

  【MajorCelltype】(7 类):
      Immune cells: 203112
      Epithelial cells: 195888
      Neural cells: 179692
      Stromal cells: 129474
      Muscle cells: 52194
      Endothelial cells: 32314
      Germ cells: 7206

  【MajorCelltypeID】(7 类):
      Major002: 203112
      Major003: 195888
      Major001: 179692
      Major004: 129474
      Major005: 52194
      Major007: 32314
      Major006: 7206

  【leiden_res2.0】(1337 类):
      Colon_CC47: 15102
      Colon_CC31: 5818
      Colon_CC06: 5095
      Colon_CC25: 4041
      Colon_CC08: 3709
      Colon_CC10: 3381
      Colon_CC34: 3039
      Colon_CC15: 2907
      Colon_CC20: 2870
      Spleen_CC13: 2836
      ... 共 1337 类，仅显示前 10

  【deepseek_v3.2_celltype】(175 类):
      Oligodendrocytes: 73929
      Stromal cells: 53700
      Enterocytes: 50796
      Excitatory neurons: 49591
      T cells: 43484
      B cells: 32938
      Endothelial cells: 22682
      Monocytes: 22555
      Smooth muscle cells: 22184
      Type II myonuclei: 22161
      ... 共 175 类，仅显示前 10

  【deepseek_v3.2_confidence】(3 类):
      High: 787340
      Medium: 11979
      Low: 561

  【deepseek_v3.2_Ann_Label_Standardized】(124 类):
      Oligodendrocytes: 73929
      Stromal cells: 53700
      Enterocytes: 50796
      Excitatory neurons: 50412
      T cells: 48972
      B cells: 34075
      Acinar cells: 28866
      Endothelial cells: 26719
      Monocytes: 22555
      Smooth muscle cells: 22440
      ... 共 124 类，仅显示前 10

  【deepseek_v3.2_check_is_correct】(2 类):
      True: 640552
      False: 159328

  【deepseek_v3.2_check_suggestion】(150 类):
      Oligodendrocytes: 73333
      Enterocytes: 52128
      Stromal cells: 50750
      Excitatory neurons: 43360
      Inhibitory neurons: 33228
      B cells: 33038
      T cells: 32093
      Monocytes: 28288
      Type II myonuclei: 27665
      Acinar cells: 27098
      ... 共 150 类，仅显示前 10

  【deepseek_v3.2_check_contamination】(2 类):
      False: 735124
      True: 64756

  【laca_curated_celltype_v3】(118 类):
      Oligodendrocytes: 73333
      Enterocytes: 52128
      Stromal cells: 50750
      Excitatory neurons: 43360
      T cells: 35148
      Acinar cells: 34971
      B cells: 34315
      Inhibitory neurons: 33228
      Monocytes: 28288
      Type II myonuclei: 27665
      ... 共 118 类，仅显示前 10
==========================================
Job started at: Sun Feb 15 02:57:36 AM CST 2026
Running on node: biohpc005
Working directory: /home/chendongsheng
==========================================
==========================================
Job started at: Sun Feb 15 03:19:52 AM CST 2026
Running on node: biohpc005
Working directory: /home/chendongsheng
==========================================
============================================================
📂 文件: /mnt/alamo01/projects/test_20241129/LCA/SP121/SP121.h5ad
============================================================

🔢 维度: 1245413 cells × 19739 genes

📋 obs 列 (35):
   - Org_celltype (category)
   - Tissue (category)
   - n_genes_by_counts (int64)
   - total_counts (float64)
   - total_counts_mt (float64)
   - pct_counts_mt (float64)
   - n_genes (int64)
   - FolderID (category)
   - LatinName (category)
   - Region (category)
   - cell_ontology_class (category)
   - broad_cell_class (category)
   - CommonName (category)
   - SPID (category)
   - SPRank (category)
   - TissueT1 (category)
   - TissueT2 (category)
   - TissueT3 (category)
   - TissueID (category)
   - SystemID (category)
   - System (category)
   - Celltype_Source (category)
   - Celltype (category)
   - Celltype_Abbreviation (category)
   - CelltypeID (category)
   - MajorCelltype (category)
   - MajorCelltypeID (category)
   - leiden_res2.0 (category)
   - deepseek_v3.2_celltype (category)
   - deepseek_v3.2_confidence (category)
   - deepseek_v3.2_Ann_Label_Standardized (category)
   - deepseek_v3.2_check_is_correct (category)
   - deepseek_v3.2_check_suggestion (category)
   - deepseek_v3.2_check_contamination (category)
   - laca_curated_celltype_v3 (category)

🧬 var 列 (0):

📐 obsm (降维):
   - X_pca: (1245413, 50)
   - X_umap: (1245413, 2)

📦 uns: ['FolderID_colors', 'LatinName_colors', 'Org_celltype_colors', 'Tissue_colors', 'neighbors', 'pca', 'umap']

📚 layers: ['counts']

============================================================
📊 分类列统计:
============================================================

  【Org_celltype】(339 类):
      t cell: 76019
      neutrophil: 64667
      macrophage: 57204
      memory b cell: 55493
      fibroblast: 43944
      b cell: 34952
      cd4-positive, alpha-beta t cell: 32472
      stromal cell of ovary: 31166
      cd8-positive, alpha-beta t cell: 30332
      endothelial cell: 29541
      ... 共 339 类，仅显示前 10

  【Tissue】(40 类):
      Lymph node: 130970
      Adipose: 87144
      Blood: 82242
      cerebral cortex: 79664
      Spleen: 68456
      Bladder: 55155
      Lung: 50929
      Muscle: 45564
      Ovary: 43732
      Thymus: 39409
      ... 共 40 类，仅显示前 10

  【FolderID】(54 类):
      Homo_sapiens_NA_2025_Rank012: 123211
      Homo_sapiens_NA_2025_Rank006: 87144
      Homo_sapiens_NA_2025_Rank002: 80838
      Homo_sapiens_NA_2025_Rank021: 63954
      Homo_sapiens_NA_2025_Rank011: 50929
      Homo_sapiens_NA_2025_Rank001: 47665
      Homo_sapiens_NA_2025_Rank015: 43732
      Homo_sapiens_NA_2025_Rank014: 39846
      Homo_sapiens_NA_2025_Rank024: 39409
      Homo_sapiens_40849297_2025_Rank001: 33719
      ... 共 54 类，仅显示前 10

  【LatinName】(1 类):
      Homo sapiens: 1245413

  【Region】(9 类):
      CBL: 27787
      CA1U: 26805
      V1C: 23724
      A46: 20561
      ANC: 19011
      S1C: 17878
      A1C: 17501
      NAC: 10203
      HTHma: 4971

  【cell_ontology_class】(174 类):
      b cell: 110282
      cd4-positive, alpha-beta t cell: 92676
      fibroblast: 72753
      cd8-positive, alpha-beta t cell: 71147
      neutrophil: 67071
      macrophage: 54857
      stromal cell of ovary: 34430
      endothelial cell: 28440
      basal cell: 23514
      monocyte: 22068
      ... 共 174 类，仅显示前 10

  【broad_cell_class】(38 类):
      t cell: 196081
      lymphocyte of b lineage: 130974
      myeloid leukocyte: 107343
      fibroblast: 88528
      granulocyte: 74581
      endothelial cell: 53403
      contractile cell: 44717
      stromal cell: 36580
      stem cell: 35000
      epithelial cell: 25068
      ... 共 38 类，仅显示前 10

  【CommonName】(1 类):
      Human: 1245413

  【SPID】(1 类):
      SP121: 1245413

  【SPRank】(1 类):
      0.0: 1245413

  【TissueT1】(31 类):
      Brain: 168441
      Lymph node: 130970
      Adipose: 87144
      Blood: 82242
      Spleen: 68456
      Bladder: 55155
      Lung: 50929
      Intestine: 50110
      Muscle: 45564
      Ovary: 43732
      ... 共 31 类，仅显示前 10

  【TissueT2】(37 类):
      Lymph node: 130970
      Visceral adipose: 87144
      PBMC: 82242
      Neocortex: 79664
      Spleen: 68456
      Bladder: 55155
      Lung: 50929
      Skeletal muscle: 45564
      Ovary: 43732
      Thymus: 39409
      ... 共 37 类，仅显示前 10

  【TissueT3】(40 类):
      Lymph node: 130970
      Visceral adipose: 87144
      PBMC: 82242
      Spleen: 68456
      Bladder: 55155
      Lung: 50929
      Skeletal muscle: 45564
      Ovary: 43732
      Thymus: 39409
      Stomach: 36968
      ... 共 40 类，仅显示前 10

  【TissueID】(40 类):
      sys02tis05: 130970
      sys07tis05: 87144
      sys02tis03: 82242
      sys02tis04: 68456
      sys09tis02: 55155
      sys04tis01: 50929
      sys08tis01: 45564
      sys06tis06: 43732
      sys02tis01: 39409
      sys05tis03: 36968
      ... 共 40 类，仅显示前 10

  【SystemID】(10 类):
      sys02: 346387
      sys01: 231795
      sys05: 176913
      sys06: 112484
      sys07: 87144
      sys04: 76554
      sys09: 68320
      sys08: 62054
      sys03: 58367
      sys10: 25395

  【System】(10 类):
      Immune system: 346387
      Nervous system: 231795
      Digestive system: 176913
      Reproductive system: 112484
      Endocrine system: 87144
      Respiratory system: 76554
      Urinary system: 68320
      Motor system: 62054
      Cardiovascular system: 58367
      Sensory system: 25395

  【Celltype_Source】(2 类):
      mapping: 1103933
      annotation: 141480

  【Celltype】(106 类):
      T_NKT cells: 203113
      B cells: 120160
      Fibroblasts: 79878
      Endothelial cells: 73521
      Neutrophils: 67093
      Macrophages: 63673
      Monocytes: 49159
      Stromal cells: 43525
      Inhibitory neurons: 40994
      Excitatory neurons: 40499
      ... 共 106 类，仅显示前 10

  【Celltype_Abbreviation】(105 类):
      T_NKT: 203113
      B: 120160
      Fibro: 79878
      Endo: 73521
      Neutro: 67093
      Macro: 63673
      Mono: 49159
      Stromal: 43525
      IN: 40994
      EX: 40499
      ... 共 105 类，仅显示前 10

  【CelltypeID】(105 类):
      Major002CT022B: 203113
      Major002CT001A: 120160
      Major004CT007A: 79878
      Major007CT001A: 73521
      Major002CT019A: 67093
      Major002CT012A: 63673
      Major002CT016A: 49159
      Major004CT026A: 43525
      Major001CT014A: 40994
      Major001CT009A: 40499
      ... 共 105 类，仅显示前 10

  【MajorCelltype】(7 类):
      Immune cells: 578917
      Stromal cells: 217548
      Epithelial cells: 161030
      Neural cells: 159386
      Endothelial cells: 73521
      Muscle cells: 35232
      Germ cells: 5614

  【MajorCelltypeID】(7 类):
      Major002: 578917
      Major004: 217548
      Major003: 161030
      Major001: 159386
      Major007: 73521
      Major005: 35232
      Major006: 5614

  【leiden_res2.0】(1839 类):
      Lymph node_CC10: 7155
      Lymph node_CC37: 6242
      Lymph node_CC20: 5735
      Lymph node_CC14: 5690
      Lymph node_CC45: 5616
      Visceral adipose_CC46: 5416
      PBMC_CC48: 5153
      Lymph node_CC50: 4726
      Lymph node_CC01: 4709
      Lymph node_CC42: 4678
      ... 共 1839 类，仅显示前 10

  【deepseek_v3.2_celltype】(177 类):
      T cells: 121152
      B cells: 105251
      Stromal cells: 81856
      Endothelial cells: 71373
      Macrophages: 69910
      Monocytes: 65564
      Excitatory neurons: 52431
      Inhibitory neurons: 47939
      Fibroblasts: 46726
      T/NKT cells: 41688
      ... 共 177 类，仅显示前 10

  【deepseek_v3.2_confidence】(2 类):
      High: 1241278
      Medium: 4135

  【deepseek_v3.2_Ann_Label_Standardized】(118 类):
      T cells: 139577
      B cells: 118020
      Stromal cells: 81856
      Endothelial cells: 72794
      Macrophages: 71746
      Monocytes: 65868
      Excitatory neurons: 52431
      Fibroblasts: 48564
      Inhibitory neurons: 47939
      T_NKT cells: 43162
      ... 共 118 类，仅显示前 10

  【deepseek_v3.2_check_is_correct】(2 类):
      True: 889685
      False: 355728

  【deepseek_v3.2_check_suggestion】(144 类):
      B cells: 106873
      Stromal cells: 103231
      T/NKT cells: 102974
      T cells: 75042
      Endothelial cells: 72718
      Macrophages: 71024
      Inhibitory neurons: 54598
      Monocytes: 50833
      Excitatory neurons: 44819
      Fibroblasts: 44729
      ... 共 144 类，仅显示前 10

  【deepseek_v3.2_check_contamination】(2 类):
      False: 1151316
      True: 94097

  【laca_curated_celltype_v3】(108 类):
      B cells: 118531
      T_NKT cells: 108545
      Stromal cells: 103231
      T cells: 88930
      Endothelial cells: 74078
      Macrophages: 71217
      Inhibitory neurons: 54598
      Neutrophils: 53764
      Monocytes: 51056
      Excitatory neurons: 44819
      ... 共 108 类，仅显示前 10
==========================================
Job started at: Sun Feb 15 03:51:07 AM CST 2026
Running on node: biohpc007
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP121
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP121/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP121/SP121.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 1,245,413 cells × 19,739 genes
   📋 obs columns: 35
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 339 unique values
      - Tissue: 40 unique values
      - n_genes_by_counts: 5800 unique values
      - total_counts: 41524 unique values
      - total_counts_mt: 4924 unique values
      - pct_counts_mt: 934556 unique values
      - n_genes: 5800 unique values
      - FolderID: 54 unique values
      - LatinName: 1 unique values
      - Region: 9 unique values
      ... and 25 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (1245413, 2)
   X range: [-6.79, 27.55]
   Y range: [-9.70, 28.35]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 108
   Mapped unique types: 108

   Sample mappings:
      "Inflammatory Chondrocytes" → "Inflammatory chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"
      "Effector Chondrocytes" → "Effector chondrocytes"
      "Hypertrophic Chondrocytes" → "Hypertrophic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             15    176,762
   Immune cells             20    581,269
   Epithelial cells         38    147,936
   Stromal cells            20    213,584
   Muscle cells              6     43,282
   Germ cells                2      5,621
   Endothelial cells         1     74,078
   Other                     6      2,881
   Other                     6      2,881
   ────────────────────────────────────────
   TOTAL                   108  1,245,413

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/umap.bin.gz (gzip compressed)...
   ✅ 1,245,413 cells × 10 bytes
   📦 Uncompressed: 11.88 MB
   📦 Compressed:   9.23 MB (22.3% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/umap_meta.json ...
   ✅ 16.9 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/celltype_legend.json ...
   ✅ 20.8 KB

🔍 Verification (first 3 cells):
   Cell 0: (   12.56,    24.65) idx= 22 "Macrophages" ✅
   Cell 1: (   12.13,    23.82) idx= 22 "Macrophages" ✅
   Cell 2: (    8.00,    26.98) idx= 32 "T_NKT cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 40 tissues
      - Lymph node: 130,970 cells
      - Adipose: 87,144 cells
      - Blood: 82,242 cells
      - cerebral cortex: 79,664 cells
      - Spleen: 68,456 cells
      ... and 35 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP121/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 1,245,413 cells × 19,739 genes

💾 gene_list.json: 19,739 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 19,739 genes

   📊 Summary:
      gene_list.json   : 183.2 KB
      genes/*.bin.gz   : 1 files, 158.5 KB total
      Uncompressed     : ~4864.9 KB
      Compression      : 96.7% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP121/

📄 Generated files:
   SP121/
   ├── umap.bin.gz           (9.23 MB)
   ├── umap_meta.json        (16.9 KB)
   ├── celltype_legend.json  (20.8 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (183.2 KB, 19,739 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP121
   • Total cells:       1,245,413
   • Cell types:              108
   • Genes (total):        19,739
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 19,739 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP121


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP075
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP075/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP075/SP075.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 1,144,691 cells × 14,896 genes
   📋 obs columns: 28
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 205 unique values
      - Tissue: 45 unique values
      - n_genes: 4725 unique values
      - FolderID: 45 unique values
      - LatinName: 1 unique values
      - CommonName: 1 unique values
      - SPID: 1 unique values
      - SPRank: 1 unique values
      - TissueT1: 37 unique values
      - TissueT2: 45 unique values
      ... and 18 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (1144691, 2)
   X range: [-9.72, 24.99]
   Y range: [-15.60, 20.56]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 131
   Mapped unique types: 131

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             23    189,573
   Immune cells             22     91,801
   Epithelial cells         58    572,835
   Stromal cells            12    141,093
   Muscle cells              8     98,042
   Germ cells                4      1,771
   Endothelial cells         1     48,024
   Other                     3      1,552
   Other                     3      1,552
   ────────────────────────────────────────
   TOTAL                   131  1,144,691

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/umap.bin.gz (gzip compressed)...
   ✅ 1,144,691 cells × 10 bytes
   📦 Uncompressed: 10.92 MB
   📦 Compressed:   8.45 MB (22.6% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/umap_meta.json ...
   ✅ 20.3 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/celltype_legend.json ...
   ✅ 24.3 KB

🔍 Verification (first 3 cells):
   Cell 0: (    6.64,    -3.00) idx=104 "Adipocytes" ✅
   Cell 1: (    6.59,    -1.63) idx=104 "Adipocytes" ✅
   Cell 2: (   11.03,   -14.62) idx=122 "Type II myonuclei" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 45 tissues
      - Cerebellum: 84,619 cells
      - Liver: 83,176 cells
      - Salivary gland: 74,320 cells
      - Visceral adipose: 66,515 cells
      - Uterus: 55,252 cells
      ... and 40 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP075/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 1,144,691 cells × 14,896 genes

💾 gene_list.json: 14,896 genes

📦 Exporting only the FIRST gene: "A2M" (gzip compressed)
   💡 Use --all-genes to export all 14,896 genes

   📊 Summary:
      gene_list.json   : 135.7 KB
      genes/*.bin.gz   : 1 files, 531.2 KB total
      Uncompressed     : ~4471.4 KB
      Compression      : 88.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP075/

📄 Generated files:
   SP075/
   ├── umap.bin.gz           (8.45 MB)
   ├── umap_meta.json        (20.3 KB)
   ├── celltype_legend.json  (24.3 KB)
   ├── tissue_info.json      (2.7 KB)
   ├── config.json
   ├── gene_list.json        (135.7 KB, 14,896 genes)
   └── genes/
       └── A2M.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP075
   • Total cells:       1,144,691
   • Cell types:              131
   • Genes (total):        14,896
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 14,896 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP075


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP126
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP126/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP126/SP126.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 483,358 cells × 16,460 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 0 unique values
      - Tissue: 15 unique values
      - n_genes: 5493 unique values
      - FolderID: 16 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 54 unique values
      - celltypist_over_clustering: 595 unique values
      - celltypist_majority_voting: 41 unique values
      - leiden_res1.0: 402 unique values
      - deepseek_v3.2_celltype: 81 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (483358, 2)
   X range: [-8.53, 28.46]
   Y range: [-10.61, 22.16]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 59
   Mapped unique types: 59

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             12     15,322
   Immune cells             15    104,107
   Epithelial cells         15     14,763
   Stromal cells             6    170,931
   Muscle cells              4     96,388
   Germ cells                2      1,763
   Endothelial cells         1     79,407
   Other                     4        677
   Other                     4        677
   ────────────────────────────────────────
   TOTAL                    59    483,358

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/umap.bin.gz (gzip compressed)...
   ✅ 483,358 cells × 10 bytes
   📦 Uncompressed: 4.61 MB
   📦 Compressed:   3.72 MB (19.3% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/umap_meta.json ...
   ✅ 9.7 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/celltype_legend.json ...
   ✅ 11.9 KB

🔍 Verification (first 3 cells):
   Cell 0: (   27.07,     3.04) idx= 50 "Smooth muscle cells" ✅
   Cell 1: (   24.29,     6.25) idx= 17 "Macrophages" ✅
   Cell 2: (   26.07,     6.63) idx= 47 "Stromal cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 15 tissues
      - Heart: 327,313 cells
      - Aorta: 43,752 cells
      - Spleen: 14,659 cells
      - PBMC: 12,826 cells
      - WAT: 12,391 cells
      ... and 10 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP126/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 483,358 cells × 16,460 genes

💾 gene_list.json: 16,460 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,460 genes

   📊 Summary:
      gene_list.json   : 150.2 KB
      genes/*.bin.gz   : 1 files, 6.8 KB total
      Uncompressed     : ~1888.1 KB
      Compression      : 99.6% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP126/

📄 Generated files:
   SP126/
   ├── umap.bin.gz           (3.72 MB)
   ├── umap_meta.json        (9.7 KB)
   ├── celltype_legend.json  (11.9 KB)
   ├── tissue_info.json      (0.9 KB)
   ├── config.json
   ├── gene_list.json        (150.2 KB, 16,460 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP126
   • Total cells:         483,358
   • Cell types:               59
   • Genes (total):        16,460
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,460 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP126


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP124
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP124/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP124/SP124.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 525,763 cells × 16,867 genes
   📋 obs columns: 36
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 309 unique values
      - Tissue: 25 unique values
      - Region: 5 unique values
      - BrainRegion: 8 unique values
      - DevoStage: 1 unique values
      - Timing: 8 unique values
      - n_genes_by_counts: 5619 unique values
      - total_counts: 69042 unique values
      - total_counts_mt: 1756 unique values
      - pct_counts_mt: 382500 unique values
      ... and 26 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (525763, 2)
   X range: [-12.68, 20.72]
   Y range: [-14.54, 18.34]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 83
   Mapped unique types: 83

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             16    434,954
   Immune cells             21     39,854
   Epithelial cells         26     21,827
   Stromal cells             8     15,008
   Muscle cells              4      1,676
   Germ cells                2      1,246
   Endothelial cells         1     10,004
   Other                     5      1,194
   Other                     5      1,194
   ────────────────────────────────────────
   TOTAL                    83    525,763

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/umap.bin.gz (gzip compressed)...
   ✅ 525,763 cells × 10 bytes
   📦 Uncompressed: 5.01 MB
   📦 Compressed:   3.87 MB (22.9% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/umap_meta.json ...
   ✅ 13.2 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/celltype_legend.json ...
   ✅ 16.2 KB

🔍 Verification (first 3 cells):
   Cell 0: (   11.88,    10.36) idx=  8 "Inhibitory neurons" ✅
   Cell 1: (   11.76,    10.66) idx=  8 "Inhibitory neurons" ✅
   Cell 2: (   11.68,    10.16) idx=  8 "Inhibitory neurons" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 25 tissues
      - Brain: 440,947 cells
      - Spleen: 11,252 cells
      - Tongue: 8,834 cells
      - Marrow: 8,503 cells
      - Retina: 7,682 cells
      ... and 20 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP124/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 525,763 cells × 16,867 genes

💾 gene_list.json: 16,867 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,867 genes

   📊 Summary:
      gene_list.json   : 154.4 KB
      genes/*.bin.gz   : 1 files, 9.5 KB total
      Uncompressed     : ~2053.8 KB
      Compression      : 99.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP124/

📄 Generated files:
   SP124/
   ├── umap.bin.gz           (3.87 MB)
   ├── umap_meta.json        (13.2 KB)
   ├── celltype_legend.json  (16.2 KB)
   ├── tissue_info.json      (1.5 KB)
   ├── config.json
   ├── gene_list.json        (154.4 KB, 16,867 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP124
   • Total cells:         525,763
   • Cell types:               83
   • Genes (total):        16,867
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,867 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP124

==========================================
Job finished at: Sun Feb 15 03:59:29 AM CST 2026
==========================================
==========================================
Job started at: Sun Feb 15 04:15:25 AM CST 2026
Running on node: biohpc004
Working directory: /home/chendongsheng
==========================================

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP013
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP013/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP013/SP013.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 1,020,185 cells × 16,720 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 55 unique values
      - Tissue: 40 unique values
      - n_genes: 4013 unique values
      - FolderID: 76 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 71 unique values
      - celltypist_over_clustering: 310 unique values
      - celltypist_majority_voting: 52 unique values
      - leiden_res1.0: 840 unique values
      - deepseek_v3.2_celltype: 123 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (1020185, 2)
   X range: [-13.72, 20.57]
   Y range: [-14.21, 20.13]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 71
   Mapped unique types: 71

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             12     63,261
   Immune cells             16    347,194
   Epithelial cells         27    236,806
   Stromal cells             8    171,241
   Muscle cells              2     51,479
   Endothelial cells         1    141,534
   Other                     5      8,670
   Other                     5      8,670
   ────────────────────────────────────────
   TOTAL                    71  1,020,185

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP013/umap.bin.gz (gzip compressed)...
   ✅ 1,020,185 cells × 10 bytes
   📦 Uncompressed: 9.73 MB
   📦 Compressed:   7.77 MB (20.1% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP013/umap_meta.json ...
   ✅ 11.5 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP013/celltype_legend.json ...
   ✅ 14.1 KB

🔍 Verification (first 3 cells):
   Cell 0: (   14.10,    12.22) idx= 39 "Epithelial cells" ✅
   Cell 1: (   13.48,    12.10) idx= 39 "Epithelial cells" ✅
   Cell 2: (   16.83,     8.70) idx= 65 "Endothelial cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 40 tissues
      - Liver: 60,915 cells
      - Omasum: 40,419 cells
      - Esophage: 38,883 cells
      - Ileum: 38,621 cells
      - Bone_marrow: 37,376 cells
      ... and 35 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP013/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 1,020,185 cells × 16,720 genes

💾 gene_list.json: 16,720 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,720 genes

   📊 Summary:
      gene_list.json   : 152.5 KB
      genes/*.bin.gz   : 1 files, 4.5 KB total
      Uncompressed     : ~3985.1 KB
      Compression      : 99.9% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP013/

📄 Generated files:
   SP013/
   ├── umap.bin.gz           (7.77 MB)
   ├── umap_meta.json        (11.5 KB)
   ├── celltype_legend.json  (14.1 KB)
   ├── tissue_info.json      (2.5 KB)
   ├── config.json
   ├── gene_list.json        (152.5 KB, 16,720 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP013
   • Total cells:       1,020,185
   • Cell types:               71
   • Genes (total):        16,720
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,720 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP013


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP014
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP014/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP014/SP014.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 198,684 cells × 3,000 genes
   📋 obs columns: 616
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - CELL: 7147 unique values
      - Species: 1 unique values
      - UMAP1: 7146 unique values
      - UMAP2: 7146 unique values
      - Org_celltype: 17 unique values
      - nUMI: 2271 unique values
      - Pseudotime: 5890 unique values
      - X_Y_classification: 1 unique values
      - Tissue: 2 unique values
      - LatinName: 1 unique values
      ... and 606 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (198684, 2)
   X range: [-12.87, 13.24]
   Y range: [-13.89, 14.29]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP015
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP015/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP015/SP015.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 34,095 cells × 3,000 genes
   📋 obs columns: 615
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - CELL: 9609 unique values
      - Species: 1 unique values
      - UMAP1: 9608 unique values
      - UMAP2: 9607 unique values
      - Org_celltype: 16 unique values
      - nUMI: 2855 unique values
      - Pseudotime: 9222 unique values
      - X_Y_classification: 1 unique values
      - Tissue: 2 unique values
      - LatinName: 1 unique values
      ... and 605 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (34095, 2)
   X range: [-3.31, 16.81]
   Y range: [-2.40, 13.74]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP017
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP017/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP017/SP017.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 82,873 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - n_genes: 5570 unique values
      - doublet_scores: 399 unique values
      - predicted_doublets: 1 unique values
      - leiden: 42 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (82873, 2)
   X range: [-11.73, 17.59]
   Y range: [-11.62, 18.44]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP020
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP020/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP020/SP020.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 799,880 cells × 17,305 genes
   📋 obs columns: 38
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 95 unique values
      - SpecieID: 2 unique values
      - RegionID: 49 unique values
      - Double_score: 38398 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5801 unique values
      - total_counts: 23212 unique values
      - total_counts_mt: 1 unique values
      - pct_counts_mt: 1 unique values
      - n_genes: 5801 unique values
      ... and 28 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (799880, 2)
   X range: [-13.19, 18.79]
   Y range: [-14.45, 16.10]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 118
   Mapped unique types: 118

   Sample mappings:
      "Fibrocartilage Chondrocytes" → "Fibrocartilage chondrocytes"
      "Inflammatory Chondrocytes" → "Inflammatory chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             21    194,632
   Immune cells             20    186,802
   Epithelial cells         43    206,138
   Stromal cells            20    115,071
   Muscle cells              7     60,443
   Germ cells                2      7,040
   Endothelial cells         1     26,802
   Other                     4      2,952
   Other                     4      2,952
   ────────────────────────────────────────
   TOTAL                   118    799,880

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP020/umap.bin.gz (gzip compressed)...
   ✅ 799,880 cells × 10 bytes
   📦 Uncompressed: 7.63 MB
   📦 Compressed:   5.97 MB (21.7% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP020/umap_meta.json ...
   ✅ 18.3 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP020/celltype_legend.json ...
   ✅ 22.1 KB

🔍 Verification (first 3 cells):
   Cell 0: (    1.27,    -5.30) idx= 71 "Neuroendocrine cells" ✅
   Cell 1: (    1.17,    -4.33) idx= 41 "Acinar cells" ✅
   Cell 2: (    3.19,    -0.93) idx=102 "Stromal cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 38 tissues
      - Neocortex: 77,748 cells
      - Colon: 72,748 cells
      - Stomach: 39,716 cells
      - Spleen: 35,195 cells
      - Cartilage: 31,202 cells
      ... and 33 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP020/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 799,880 cells × 17,305 genes

💾 gene_list.json: 17,305 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 17,305 genes

   📊 Summary:
      gene_list.json   : 158.4 KB
      genes/*.bin.gz   : 1 files, 34.5 KB total
      Uncompressed     : ~3124.5 KB
      Compression      : 98.9% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP020/

📄 Generated files:
   SP020/
   ├── umap.bin.gz           (5.97 MB)
   ├── umap_meta.json        (18.3 KB)
   ├── celltype_legend.json  (22.1 KB)
   ├── tissue_info.json      (2.3 KB)
   ├── config.json
   ├── gene_list.json        (158.4 KB, 17,305 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP020
   • Total cells:         799,880
   • Cell types:              118
   • Genes (total):        17,305
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 17,305 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP020


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP021
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP021/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP021/SP021.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 720,956 cells × 16,663 genes
   📋 obs columns: 38
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 80 unique values
      - SpecieID: 2 unique values
      - RegionID: 41 unique values
      - Double_score: 34296 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5800 unique values
      - total_counts: 23047 unique values
      - total_counts_mt: 1 unique values
      - pct_counts_mt: 1 unique values
      - n_genes: 5800 unique values
      ... and 28 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (720956, 2)
   X range: [-6.72, 25.19]
   Y range: [-10.68, 21.25]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 115
   Mapped unique types: 115

   Sample mappings:
      "Fibrocartilage Chondrocytes" → "Fibrocartilage chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"
      "Inflammatory Chondrocytes" → "Inflammatory chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             18    200,352
   Immune cells             18    170,388
   Epithelial cells         46    162,109
   Stromal cells            19     93,428
   Muscle cells              8     59,347
   Germ cells                4      8,394
   Endothelial cells         1     26,829
   Other                     1        109
   Other                     1        109
   ────────────────────────────────────────
   TOTAL                   115    720,956

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP021/umap.bin.gz (gzip compressed)...
   ✅ 720,956 cells × 10 bytes
   📦 Uncompressed: 6.88 MB
   📦 Compressed:   5.35 MB (22.2% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP021/umap_meta.json ...
   ✅ 17.9 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP021/celltype_legend.json ...
   ✅ 21.1 KB

🔍 Verification (first 3 cells):
   Cell 0: (   10.80,     1.12) idx=113 "Endothelial cells" ✅
   Cell 1: (   18.99,     4.90) idx= 78 "Serous cells" ✅
   Cell 2: (   17.21,     5.97) idx= 35 "T_NKT cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 38 tissues
      - Neocortex: 83,218 cells
      - Thyroid: 25,589 cells
      - Pituitary gland: 24,845 cells
      - Pancreas: 23,105 cells
      - Spleen: 21,486 cells
      ... and 33 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP021/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 720,956 cells × 16,663 genes

💾 gene_list.json: 16,663 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,663 genes

   📊 Summary:
      gene_list.json   : 151.7 KB
      genes/*.bin.gz   : 1 files, 26.1 KB total
      Uncompressed     : ~2816.2 KB
      Compression      : 99.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP021/

📄 Generated files:
   SP021/
   ├── umap.bin.gz           (5.35 MB)
   ├── umap_meta.json        (17.9 KB)
   ├── celltype_legend.json  (21.1 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (151.7 KB, 16,663 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP021
   • Total cells:         720,956
   • Cell types:              115
   • Genes (total):        16,663
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,663 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP021


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP024
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP024/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP024/SP024.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 297,047 cells × 8,970 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 279 unique values
      - Tissue: 17 unique values
      - n_genes: 3667 unique values
      - FolderID: 17 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 60 unique values
      - celltypist_over_clustering: 477 unique values
      - celltypist_majority_voting: 40 unique values
      - leiden_res1.0: 290 unique values
      - deepseek_v3.2_celltype: 90 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (297047, 2)
   X range: [-8.97, 22.81]
   Y range: [-8.20, 24.21]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 61
   Mapped unique types: 61

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             10     11,008
   Immune cells             13    118,665
   Epithelial cells         22     79,165
   Stromal cells             5     41,081
   Muscle cells              4      8,177
   Germ cells                3     20,497
   Endothelial cells         1     12,778
   Other                     3      5,676
   Other                     3      5,676
   ────────────────────────────────────────
   TOTAL                    61    297,047

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP024/umap.bin.gz (gzip compressed)...
   ✅ 297,047 cells × 10 bytes
   📦 Uncompressed: 2.83 MB
   📦 Compressed:   2.20 MB (22.4% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP024/umap_meta.json ...
   ✅ 10.0 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP024/celltype_legend.json ...
   ✅ 12.1 KB

🔍 Verification (first 3 cells):
   Cell 0: (   13.50,    12.64) idx= 19 "Plasma B cells" ✅
   Cell 1: (   13.37,    12.64) idx= 19 "Plasma B cells" ✅
   Cell 2: (   13.32,    12.28) idx= 19 "Plasma B cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 17 tissues
      - Bone marrow: 31,563 cells
      - Spleen: 25,179 cells
      - Brain: 23,904 cells
      - Pancreas: 22,275 cells
      - Heart: 21,621 cells
      ... and 12 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP024/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 297,047 cells × 8,970 genes

💾 gene_list.json: 8,970 genes

📦 Exporting only the FIRST gene: "A1CF" (gzip compressed)
   💡 Use --all-genes to export all 8,970 genes

   📊 Summary:
      gene_list.json   : 81.0 KB
      genes/*.bin.gz   : 1 files, 2.0 KB total
      Uncompressed     : ~1160.3 KB
      Compression      : 99.8% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP024/

📄 Generated files:
   SP024/
   ├── umap.bin.gz           (2.20 MB)
   ├── umap_meta.json        (10.0 KB)
   ├── celltype_legend.json  (12.1 KB)
   ├── tissue_info.json      (1.0 KB)
   ├── config.json
   ├── gene_list.json        (81.0 KB, 8,970 genes)
   └── genes/
       └── A1CF.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP024
   • Total cells:         297,047
   • Cell types:               61
   • Genes (total):         8,970
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 8,970 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP024


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP025
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP025/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP025/SP025.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 44,570 cells × 3,000 genes
   📋 obs columns: 592
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 3 unique values
      - BrainRegion: 5 unique values
      - DevoStage: 1 unique values
      - CellType: 5 unique values
      - n_genes: 3775 unique values
      - leiden: 33 unique values
      - UMAP_X: 19996 unique values
      - UMAP_Y: 19997 unique values
      ... and 582 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (44570, 2)
   X range: [-9.06, 16.31]
   Y range: [-11.32, 13.83]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP026
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP026/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP026/SP026.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 6,300 cells × 3,000 genes
   📋 obs columns: 590
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Tissue: 1 unique values
      - Region: 3 unique values
      - BrainRegion: 4 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 11 unique values
      - CellType: 11 unique values
      - n_genes: 1088 unique values
      - doublet_scores: 140 unique values
      - predicted_doublets: 1 unique values
      - leiden: 14 unique values
      ... and 580 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (6300, 2)
   X range: [-9.05, 18.54]
   Y range: [-11.78, 19.07]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP029
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP029/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP029/SP029.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 5,914 cells × 3,000 genes
   📋 obs columns: 597
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Unnamed: 0.1: 4127 unique values
      - Unnamed: 0: 4127 unique values
      - Sample_ID: 18 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - BrainRegion: 2 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 10 unique values
      - CellType: 10 unique values
      - n_genes: 1962 unique values
      ... and 587 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (5914, 2)
   X range: [-6.19, 19.08]
   Y range: [-12.87, 18.61]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP030
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP030/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP030/SP030.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 34,480 cells × 3,000 genes
   📋 obs columns: 598
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 4 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 3 unique values
      - CellType: 4 unique values
      - Anno_Fish: 4 unique values
      - n_genes: 5423 unique values
      - doublet_scores: 477 unique values
      - predicted_doublets: 1 unique values
      ... and 588 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (34480, 2)
   X range: [-9.40, 13.49]
   Y range: [-5.80, 17.88]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP037
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP037/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP037/SP037.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 209,615 cells × 16,630 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 0 unique values
      - Tissue: 17 unique values
      - n_genes: 3920 unique values
      - FolderID: 17 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 49 unique values
      - celltypist_over_clustering: 878 unique values
      - celltypist_majority_voting: 36 unique values
      - leiden_res1.0: 213 unique values
      - deepseek_v3.2_celltype: 77 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (209615, 2)
   X range: [-11.58, 23.54]
   Y range: [-9.05, 19.61]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 48
   Mapped unique types: 48

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              4      1,183
   Immune cells              7     30,283
   Epithelial cells         23     88,216
   Stromal cells             6     26,958
   Muscle cells              3     27,987
   Germ cells                2        679
   Endothelial cells         1     33,838
   Other                     2        471
   Other                     2        471
   ────────────────────────────────────────
   TOTAL                    48    209,615

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP037/umap.bin.gz (gzip compressed)...
   ✅ 209,615 cells × 10 bytes
   📦 Uncompressed: 2.00 MB
   📦 Compressed:   1.59 MB (20.7% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP037/umap_meta.json ...
   ✅ 8.1 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP037/celltype_legend.json ...
   ✅ 9.7 KB

🔍 Verification (first 3 cells):
   Cell 0: (   18.41,    -4.97) idx= 40 "Cardiomyocytes" ✅
   Cell 1: (   19.30,    -5.37) idx= 40 "Cardiomyocytes" ✅
   Cell 2: (   19.09,    -4.01) idx= 40 "Cardiomyocytes" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 17 tissues
      - Testis: 69,390 cells
      - Liver: 26,300 cells
      - Pancreas: 22,226 cells
      - Lung: 17,078 cells
      - Ventricle: 16,984 cells
      ... and 12 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP037/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 209,615 cells × 16,630 genes

💾 gene_list.json: 16,630 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,630 genes

   📊 Summary:
      gene_list.json   : 151.7 KB
      genes/*.bin.gz   : 1 files, 4.0 KB total
      Uncompressed     : ~818.8 KB
      Compression      : 99.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP037/

📄 Generated files:
   SP037/
   ├── umap.bin.gz           (1.59 MB)
   ├── umap_meta.json        (8.1 KB)
   ├── celltype_legend.json  (9.7 KB)
   ├── tissue_info.json      (1.0 KB)
   ├── config.json
   ├── gene_list.json        (151.7 KB, 16,630 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP037
   • Total cells:         209,615
   • Cell types:               48
   • Genes (total):        16,630
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,630 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP037


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP038
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP038/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP038/SP038.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 21,539 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2521 unique values
      - doublet_scores: 281 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (21539, 2)
   X range: [-4.67, 18.52]
   Y range: [-11.61, 16.41]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP039
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP039/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP039/SP039.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 132,688 cells × 3,000 genes
   📋 obs columns: 623
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - UMAP1: 9888 unique values
      - UMAP2: 9888 unique values
      - Org_celltype: 19 unique values
      - nUMI: 3338 unique values
      - Pseudotime: 5544 unique values
      - X_Y_classification: 3 unique values
      - Tissue: 3 unique values
      - LatinName: 1 unique values
      - n_genes: 5660 unique values
      - doublet_scores: 1010 unique values
      ... and 613 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (132688, 2)
   X range: [-6.86, 15.85]
   Y range: [-8.16, 15.36]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP053
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP053/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP053/SP053.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 80,000 cells × 3,000 genes
   📋 obs columns: 472
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 24 unique values
      - nCount_RNA: 15048 unique values
      - nFeature_RNA: 3768 unique values
      - Percent.Largest.Gene: 75703 unique values
      - Doubletscore: 71 unique values
      - Predicted_doublets: 1 unique values
      - integrated_snn_res.1: 53 unique values
      - integrated_snn_res.2: 68 unique values
      - integrated_snn_res.3: 89 unique values
      - seurat_clusters: 93 unique values
      ... and 462 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (80000, 2)
   X range: [-6.59, 14.58]
   Y range: [-1.06, 14.90]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP056
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP056/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP056/SP056.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 557 cells × 3,001 genes
   📋 obs columns: 513
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 50 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Timing: 7 unique values
      - n_genes: 503 unique values
      - doublet_scores: 25 unique values
      - predicted_doublets: 1 unique values
      - leiden: 10 unique values
      - UMAP_X: 557 unique values
      ... and 503 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (557, 2)
   X range: [-5.48, 13.80]
   Y range: [7.90, 17.36]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP075
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP075/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP075/SP075.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 1,144,691 cells × 14,896 genes
   📋 obs columns: 28
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 205 unique values
      - Tissue: 45 unique values
      - n_genes: 4725 unique values
      - FolderID: 45 unique values
      - LatinName: 1 unique values
      - CommonName: 1 unique values
      - SPID: 1 unique values
      - SPRank: 1 unique values
      - TissueT1: 37 unique values
      - TissueT2: 45 unique values
      ... and 18 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (1144691, 2)
   X range: [-9.72, 24.99]
   Y range: [-15.60, 20.56]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 131
   Mapped unique types: 131

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             23    189,573
   Immune cells             22     91,801
   Epithelial cells         58    572,835
   Stromal cells            12    141,093
   Muscle cells              8     98,042
   Germ cells                4      1,771
   Endothelial cells         1     48,024
   Other                     3      1,552
   Other                     3      1,552
   ────────────────────────────────────────
   TOTAL                   131  1,144,691

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/umap.bin.gz (gzip compressed)...
   ✅ 1,144,691 cells × 10 bytes
   📦 Uncompressed: 10.92 MB
   📦 Compressed:   8.45 MB (22.6% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/umap_meta.json ...
   ✅ 20.3 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP075/celltype_legend.json ...
   ✅ 24.3 KB

🔍 Verification (first 3 cells):
   Cell 0: (    6.64,    -3.00) idx=104 "Adipocytes" ✅
   Cell 1: (    6.59,    -1.63) idx=104 "Adipocytes" ✅
   Cell 2: (   11.03,   -14.62) idx=122 "Type II myonuclei" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 45 tissues
      - Cerebellum: 84,619 cells
      - Liver: 83,176 cells
      - Salivary gland: 74,320 cells
      - Visceral adipose: 66,515 cells
      - Uterus: 55,252 cells
      ... and 40 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP075/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 1,144,691 cells × 14,896 genes

💾 gene_list.json: 14,896 genes

📦 Exporting only the FIRST gene: "A2M" (gzip compressed)
   💡 Use --all-genes to export all 14,896 genes

   📊 Summary:
      gene_list.json   : 135.7 KB
      genes/*.bin.gz   : 1 files, 531.2 KB total
      Uncompressed     : ~4471.4 KB
      Compression      : 88.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP075/

📄 Generated files:
   SP075/
   ├── umap.bin.gz           (8.45 MB)
   ├── umap_meta.json        (20.3 KB)
   ├── celltype_legend.json  (24.3 KB)
   ├── tissue_info.json      (2.7 KB)
   ├── config.json
   ├── gene_list.json        (135.7 KB, 14,896 genes)
   └── genes/
       └── A2M.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP075
   • Total cells:       1,144,691
   • Cell types:              131
   • Genes (total):        14,896
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 14,896 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP075


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP084
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP084/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP084/SP084.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 218,788 cells × 12,616 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 194 unique values
      - Tissue: 14 unique values
      - n_genes: 1386 unique values
      - FolderID: 14 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 41 unique values
      - celltypist_over_clustering: 412 unique values
      - celltypist_majority_voting: 23 unique values
      - leiden_res1.0: 462 unique values
      - deepseek_v3.2_celltype: 116 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (218788, 2)
   X range: [-12.93, 17.53]
   Y range: [-9.39, 21.35]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 50
   Mapped unique types: 50

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              7      9,367
   Immune cells             13     93,851
   Epithelial cells         12     70,199
   Stromal cells             5     13,755
   Muscle cells              1        723
   Germ cells                3     16,696
   Endothelial cells         1      1,039
   Other                     8     13,158
   Other                     8     13,158
   ────────────────────────────────────────
   TOTAL                    50    218,788

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP084/umap.bin.gz (gzip compressed)...
   ✅ 218,788 cells × 10 bytes
   📦 Uncompressed: 2.09 MB
   📦 Compressed:   1.70 MB (18.6% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP084/umap_meta.json ...
   ✅ 8.4 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP084/celltype_legend.json ...
   ✅ 11.0 KB

🔍 Verification (first 3 cells):
   Cell 0: (   -2.05,     0.95) idx= 17 "Monocytes" ✅
   Cell 1: (   -1.67,    -4.30) idx= 17 "Monocytes" ✅
   Cell 2: (    0.46,    -0.70) idx= 17 "Monocytes" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 14 tissues
      - Ovary: 31,496 cells
      - Skin: 29,086 cells
      - Caudal fin: 26,922 cells
      - Intestine&Pancreas: 26,170 cells
      - Brain: 20,823 cells
      ... and 9 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP084/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 218,788 cells × 12,616 genes

💾 gene_list.json: 12,616 genes

📦 Exporting only the FIRST gene: "A1CF" (gzip compressed)
   💡 Use --all-genes to export all 12,616 genes

   📊 Summary:
      gene_list.json   : 114.5 KB
      genes/*.bin.gz   : 1 files, 2.8 KB total
      Uncompressed     : ~854.6 KB
      Compression      : 99.7% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP084/

📄 Generated files:
   SP084/
   ├── umap.bin.gz           (1.70 MB)
   ├── umap_meta.json        (8.4 KB)
   ├── celltype_legend.json  (11.0 KB)
   ├── tissue_info.json      (0.9 KB)
   ├── config.json
   ├── gene_list.json        (114.5 KB, 12,616 genes)
   └── genes/
       └── A1CF.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP084
   • Total cells:         218,788
   • Cell types:               50
   • Genes (total):        12,616
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 12,616 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP084


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP085
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP085/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP085/SP085.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 190,817 cells × 3,000 genes
   📋 obs columns: 615
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - CommonName: 1 unique values
      - Timing: 4 unique values
      - Sex: 2 unique values
      - sample_id: 8 unique values
      - Org_celltype: 20 unique values
      - Tissue: 3 unique values
      - LatinName: 1 unique values
      - n_genes: 5514 unique values
      - doublet_scores: 595 unique values
      - predicted_doublets: 1 unique values
      ... and 605 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (190817, 2)
   X range: [-7.34, 16.00]
   Y range: [-7.63, 16.08]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP086
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP086/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP086/SP086.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 3,216 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 7 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 7 unique values
      - n_genes: 2129 unique values
      - doublet_scores: 71 unique values
      - predicted_doublets: 1 unique values
      - leiden: 17 unique values
      - UMAP_X: 3216 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (3216, 2)
   X range: [-19.57, 12.75]
   Y range: [-16.37, 13.48]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP087
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP087/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP087/SP087.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 40,531 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 5008 unique values
      - doublet_scores: 258 unique values
      - predicted_doublets: 1 unique values
      - leiden: 43 unique values
      - UMAP_X: 40502 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (40531, 2)
   X range: [-7.27, 21.65]
   Y range: [-10.61, 17.96]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP089
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP089/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP089/SP089.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 33,490 cells × 16,624 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 36 unique values
      - Tissue: 7 unique values
      - n_genes: 4994 unique values
      - FolderID: 7 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 32 unique values
      - celltypist_over_clustering: 142 unique values
      - celltypist_majority_voting: 22 unique values
      - leiden_res1.0: 131 unique values
      - deepseek_v3.2_celltype: 47 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (33490, 2)
   X range: [-7.84, 21.92]
   Y range: [-14.79, 18.81]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 34
   Mapped unique types: 34

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              2        477
   Immune cells              7      4,369
   Epithelial cells         16     16,714
   Stromal cells             3      2,970
   Muscle cells              4      4,563
   Germ cells                1         15
   Endothelial cells         1      4,382
   ────────────────────────────────────────
   TOTAL                    34     33,490

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP089/umap.bin.gz (gzip compressed)...
   ✅ 33,490 cells × 10 bytes
   📦 Uncompressed: 0.32 MB
   📦 Compressed:   0.26 MB (19.2% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP089/umap_meta.json ...
   ✅ 5.9 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP089/celltype_legend.json ...
   ✅ 6.7 KB

🔍 Verification (first 3 cells):
   Cell 0: (   15.30,    11.78) idx= 31 "Smooth muscle cells" ✅
   Cell 1: (   15.82,    12.69) idx= 24 "Squamous cells" ✅
   Cell 2: (   15.49,    12.34) idx= 24 "Squamous cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 7 tissues
      - Lung: 10,756 cells
      - Heart: 8,147 cells
      - Liver: 7,640 cells
      - Kidney: 2,762 cells
      - Esophagus: 1,927 cells
      ... and 2 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP089/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 33,490 cells × 16,624 genes

💾 gene_list.json: 16,624 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,624 genes

   📊 Summary:
      gene_list.json   : 152.0 KB
      genes/*.bin.gz   : 1 files, 28.8 KB total
      Uncompressed     : ~130.8 KB
      Compression      : 78.0% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP089/

📄 Generated files:
   SP089/
   ├── umap.bin.gz           (0.26 MB)
   ├── umap_meta.json        (5.9 KB)
   ├── celltype_legend.json  (6.7 KB)
   ├── tissue_info.json      (0.5 KB)
   ├── config.json
   ├── gene_list.json        (152.0 KB, 16,624 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP089
   • Total cells:          33,490
   • Cell types:               34
   • Genes (total):        16,624
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,624 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP089


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP090
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP090/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP090/SP090.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 31,055 cells × 3,000 genes
   📋 obs columns: 613
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 10 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 2 unique values
      - Old_celltype: 10 unique values
      - CellType: 10 unique values
      - n_genes: 4781 unique values
      - doublet_scores: 470 unique values
      - predicted_doublets: 1 unique values
      - leiden: 38 unique values
      ... and 603 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (31055, 2)
   X range: [-10.78, 15.99]
   Y range: [-9.44, 16.35]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP091
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP091/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP091/SP091.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 6,400 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 2414 unique values
      - doublet_scores: 107 unique values
      - predicted_doublets: 1 unique values
      - leiden: 20 unique values
      - UMAP_X: 6400 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (6400, 2)
   X range: [-10.57, 18.57]
   Y range: [-8.27, 18.10]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP092
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP092/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP092/SP092.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 7,822 cells × 3,000 genes
   📋 obs columns: 570
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 1531 unique values
      - nFeature_RNA: 977 unique values
      - Species: 1 unique values
      - Tissue: 1 unique values
      - percent.mt: 1 unique values
      - RNA_snn_res.1: 10 unique values
      - seurat_clusters: 10 unique values
      - pANN_0.25_0.2_662: 1059 unique values
      - DF.classifications_0.25_0.2_662: 1 unique values
      ... and 560 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (7822, 2)
   X range: [-10.38, 1.38]
   Y range: [-4.92, 12.18]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP094
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP094/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP094/SP094.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 198,501 cells × 3,000 genes
   📋 obs columns: 637
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 18 unique values
      - nCount_RNA: 16155 unique values
      - nFeature_RNA: 4047 unique values
      - percent.mt: 65171 unique values
      - percent.hbm: 219 unique values
      - percent.ppbp: 14752 unique values
      - percent.pal: 67254 unique values
      - S.Score: 72130 unique values
      - G2M.Score: 72133 unique values
      - Phase: 3 unique values
      ... and 627 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (198501, 2)
   X range: [-5.26, 21.07]
   Y range: [-3.09, 20.24]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP095
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP095/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP095/SP095.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 11,523 cells × 3,000 genes
   📋 obs columns: 609
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 4 unique values
      - nCount_RNA: 1413 unique values
      - nFeature_RNA: 1250 unique values
      - percent.mt: 1468 unique values
      - Species: 1 unique values
      - seurat_clusters: 18 unique values
      - Org_celltype: 18 unique values
      - integrated_snn_res.0.8: 18 unique values
      - Tissue: 1 unique values
      - LatinName: 1 unique values
      ... and 599 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (11523, 2)
   X range: [-5.41, 11.83]
   Y range: [-3.27, 18.12]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP098
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP098/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP098/SP098.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 59,925 cells × 3,000 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 6 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 52 unique values
      - Region: 2 unique values
      - Tissue: 5 unique values
      - _index: 59925 unique values
      - doublet_scores: 953 unique values
      - n_genes: 4226 unique values
      - predicted_doublets: 1 unique values

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP100
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP100/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP100/SP100.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 464 cells × 3,000 genes
   📋 obs columns: 567
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 2 unique values
      - nCount_RNA: 389 unique values
      - nFeature_RNA: 337 unique values
      - Species: 1 unique values
      - Tissue: 1 unique values
      - percent.mt: 1 unique values
      - RNA_snn_res.1: 7 unique values
      - seurat_clusters: 7 unique values
      - pANN_0.25_0.29_40: 46 unique values
      - DF.classifications_0.25_0.29_40: 1 unique values
      ... and 557 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (464, 2)
   X range: [-3.83, 9.87]
   Y range: [-9.25, 6.49]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP101
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP101/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP101/SP101.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 647,801 cells × 16,479 genes
   📋 obs columns: 38
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 78 unique values
      - SpecieID: 2 unique values
      - RegionID: 41 unique values
      - Double_score: 32143 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5791 unique values
      - total_counts: 23535 unique values
      - total_counts_mt: 2138 unique values
      - pct_counts_mt: 249796 unique values
      - n_genes: 5791 unique values
      ... and 28 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (647801, 2)
   X range: [-10.36, 22.30]
   Y range: [-11.61, 20.85]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 109
   Mapped unique types: 109

   Sample mappings:
      "Fibrocartilage Chondrocytes" → "Fibrocartilage chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             18    194,507
   Immune cells             19    190,657
   Epithelial cells         40    117,763
   Stromal cells            15     71,904
   Muscle cells              6     45,221
   Germ cells                3      4,365
   Endothelial cells         1     18,115
   Other                     7      5,269
   Other                     7      5,269
   ────────────────────────────────────────
   TOTAL                   109    647,801

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP101/umap.bin.gz (gzip compressed)...
   ✅ 647,801 cells × 10 bytes
   📦 Uncompressed: 6.18 MB
   📦 Compressed:   4.81 MB (22.1% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP101/umap_meta.json ...
   ✅ 16.9 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP101/celltype_legend.json ...
   ✅ 21.0 KB

🔍 Verification (first 3 cells):
   Cell 0: (   12.68,     9.03) idx= 64 "Mucous cells" ✅
   Cell 1: (    8.71,     9.56) idx= 90 "Stromal cells" ✅
   Cell 2: (   18.38,     6.58) idx= 36 "T_NKT cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 38 tissues
      - Neocortex: 76,933 cells
      - Pancreas: 27,197 cells
      - Mesenteric lymph nodes: 24,747 cells
      - Lung: 22,300 cells
      - Spleen: 21,036 cells
      ... and 33 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP101/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 647,801 cells × 16,479 genes

💾 gene_list.json: 16,479 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,479 genes

   📊 Summary:
      gene_list.json   : 150.5 KB
      genes/*.bin.gz   : 1 files, 12.5 KB total
      Uncompressed     : ~2530.5 KB
      Compression      : 99.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP101/

📄 Generated files:
   SP101/
   ├── umap.bin.gz           (4.81 MB)
   ├── umap_meta.json        (16.9 KB)
   ├── celltype_legend.json  (21.0 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (150.5 KB, 16,479 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP101
   • Total cells:         647,801
   • Cell types:              109
   • Genes (total):        16,479
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,479 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP101


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP105
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP105/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP105/SP105.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 312,079 cells × 17,379 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 71 unique values
      - Tissue: 21 unique values
      - n_genes: 5477 unique values
      - FolderID: 21 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 52 unique values
      - celltypist_over_clustering: 346 unique values
      - celltypist_majority_voting: 42 unique values
      - leiden_res1.0: 450 unique values
      - deepseek_v3.2_celltype: 103 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (312079, 2)
   X range: [-9.45, 23.31]
   Y range: [-12.02, 23.02]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 70
   Mapped unique types: 70

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             17     62,084
   Immune cells             18    152,933
   Epithelial cells         20     41,617
   Stromal cells             5     20,334
   Muscle cells              2      3,574
   Germ cells                3     13,392
   Endothelial cells         1     16,455
   Other                     4      1,690
   Other                     4      1,690
   ────────────────────────────────────────
   TOTAL                    70    312,079

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP105/umap.bin.gz (gzip compressed)...
   ✅ 312,079 cells × 10 bytes
   📦 Uncompressed: 2.98 MB
   📦 Compressed:   2.37 MB (20.5% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP105/umap_meta.json ...
   ✅ 11.3 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP105/celltype_legend.json ...
   ✅ 13.7 KB

🔍 Verification (first 3 cells):
   Cell 0: (    4.72,    19.68) idx= 55 "Fibroblasts" ✅
   Cell 1: (   14.09,    13.66) idx= 33 "T cells" ✅
   Cell 2: (    6.87,    22.01) idx= 55 "Fibroblasts" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 21 tissues
      - Ileum: 72,891 cells
      - Liver: 32,888 cells
      - Adipose: 29,231 cells
      - Lung: 25,725 cells
      - Spleen: 21,791 cells
      ... and 16 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP105/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 312,079 cells × 17,379 genes

💾 gene_list.json: 17,379 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 17,379 genes

   📊 Summary:
      gene_list.json   : 158.9 KB
      genes/*.bin.gz   : 1 files, 36.2 KB total
      Uncompressed     : ~1219.1 KB
      Compression      : 97.0% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP105/

📄 Generated files:
   SP105/
   ├── umap.bin.gz           (2.37 MB)
   ├── umap_meta.json        (11.3 KB)
   ├── celltype_legend.json  (13.7 KB)
   ├── tissue_info.json      (1.3 KB)
   ├── config.json
   ├── gene_list.json        (158.9 KB, 17,379 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP105
   • Total cells:         312,079
   • Cell types:               70
   • Genes (total):        17,379
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 17,379 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP105


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP107
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP107/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP107/SP107.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 137,852 cells × 3,000 genes
   📋 obs columns: 644
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 1162 unique values
      - nFeature_RNA: 1024 unique values
      - RNA_snn_res.0.2: 6 unique values
      - seurat_clusters: 32 unique values
      - integrated_snn_res.1: 32 unique values
      - Org_celltype: 86 unique values
      - Tissue: 3 unique values
      - LatinName: 1 unique values
      - n_genes: 5666 unique values
      ... and 634 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (137852, 2)
   X range: [-12.57, 13.23]
   Y range: [-11.46, 14.46]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP113
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP113/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP113/SP113.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 80,057 cells × 14,383 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 26 unique values
      - Tissue: 5 unique values
      - n_genes: 5449 unique values
      - FolderID: 5 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 24 unique values
      - celltypist_over_clustering: 292 unique values
      - celltypist_majority_voting: 15 unique values
      - leiden_res1.0: 117 unique values
      - deepseek_v3.2_celltype: 41 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (80057, 2)
   X range: [-9.22, 19.89]
   Y range: [-7.72, 23.53]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 29
   Mapped unique types: 29

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              2      1,297
   Immune cells              7     16,174
   Epithelial cells         10     17,339
   Stromal cells             3     11,107
   Muscle cells              2     22,904
   Endothelial cells         1     10,523
   Other                     4        713
   Other                     4        713
   ────────────────────────────────────────
   TOTAL                    29     80,057

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP113/umap.bin.gz (gzip compressed)...
   ✅ 80,057 cells × 10 bytes
   📦 Uncompressed: 0.76 MB
   📦 Compressed:   0.61 MB (19.6% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP113/umap_meta.json ...
   ✅ 5.3 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP113/celltype_legend.json ...
   ✅ 6.6 KB

🔍 Verification (first 3 cells):
   Cell 0: (    1.59,    18.36) idx= 27 "Proliferating cells" ✅
   Cell 1: (   10.81,    15.52) idx=  6 "Macrophages" ✅
   Cell 2: (    3.97,    21.17) idx= 22 "Cardiomyocytes" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 5 tissues
      - Spleen: 33,325 cells
      - Heart: 16,380 cells
      - Lung: 16,024 cells
      - Liver: 10,096 cells
      - Kidney: 4,232 cells
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP113/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 80,057 cells × 14,383 genes

💾 gene_list.json: 14,383 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 14,383 genes

   📊 Summary:
      gene_list.json   : 130.7 KB
      genes/*.bin.gz   : 1 files, 17.1 KB total
      Uncompressed     : ~312.7 KB
      Compression      : 94.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP113/

📄 Generated files:
   SP113/
   ├── umap.bin.gz           (0.61 MB)
   ├── umap_meta.json        (5.3 KB)
   ├── celltype_legend.json  (6.6 KB)
   ├── tissue_info.json      (0.3 KB)
   ├── config.json
   ├── gene_list.json        (130.7 KB, 14,383 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP113
   • Total cells:          80,057
   • Cell types:               29
   • Genes (total):        14,383
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 14,383 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP113


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP115
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP115/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP115/SP115.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 92,559 cells × 14,276 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 31 unique values
      - Tissue: 9 unique values
      - n_genes: 3910 unique values
      - FolderID: 9 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 28 unique values
      - celltypist_over_clustering: 288 unique values
      - celltypist_majority_voting: 15 unique values
      - leiden_res1.0: 140 unique values
      - deepseek_v3.2_celltype: 43 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (92559, 2)
   X range: [-9.69, 20.57]
   Y range: [-10.39, 22.60]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 31
   Mapped unique types: 31

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              4      3,092
   Immune cells              5      8,816
   Epithelial cells         13     18,959
   Stromal cells             3     17,518
   Muscle cells              2     28,877
   Endothelial cells         1     14,126
   Other                     3      1,171
   Other                     3      1,171
   ────────────────────────────────────────
   TOTAL                    31     92,559

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP115/umap.bin.gz (gzip compressed)...
   ✅ 92,559 cells × 10 bytes
   📦 Uncompressed: 0.88 MB
   📦 Compressed:   0.71 MB (19.7% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP115/umap_meta.json ...
   ✅ 5.6 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP115/celltype_legend.json ...
   ✅ 6.8 KB

🔍 Verification (first 3 cells):
   Cell 0: (   15.67,    16.42) idx=  0 "Enteric glial cells" ✅
   Cell 1: (   16.18,    16.20) idx= 24 "Stromal cells" ✅
   Cell 2: (   17.30,    16.62) idx= 14 "Enterocytes" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 9 tissues
      - Esophagus: 24,578 cells
      - Lung: 22,079 cells
      - Heart: 12,958 cells
      - Stomach: 12,463 cells
      - Liver: 5,693 cells
      ... and 4 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP115/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 92,559 cells × 14,276 genes

💾 gene_list.json: 14,276 genes

📦 Exporting only the FIRST gene: "A1CF" (gzip compressed)
   💡 Use --all-genes to export all 14,276 genes

   📊 Summary:
      gene_list.json   : 129.6 KB
      genes/*.bin.gz   : 1 files, 5.3 KB total
      Uncompressed     : ~361.6 KB
      Compression      : 98.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP115/

📄 Generated files:
   SP115/
   ├── umap.bin.gz           (0.71 MB)
   ├── umap_meta.json        (5.6 KB)
   ├── celltype_legend.json  (6.8 KB)
   ├── tissue_info.json      (0.6 KB)
   ├── config.json
   ├── gene_list.json        (129.6 KB, 14,276 genes)
   └── genes/
       └── A1CF.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP115
   • Total cells:          92,559
   • Cell types:               31
   • Genes (total):        14,276
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 14,276 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP115


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP116
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP116/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP116/SP116.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 795 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 1 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 1 unique values
      - n_genes: 407 unique values
      - doublet_scores: 19 unique values
      - predicted_doublets: 1 unique values
      - leiden: 11 unique values
      - UMAP_X: 795 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (795, 2)
   X range: [-1.07, 6.44]
   Y range: [0.32, 8.24]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP118
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP118/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP118/SP118.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 46,394 cells × 3,000 genes
   📋 obs columns: 617
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 74 unique values
      - Tissue: 3 unique values
      - Region: 2 unique values
      - DevoStage: 1 unique values
      - CellType: 1 unique values
      - n_genes: 4185 unique values
      - doublet_scores: 754 unique values
      - predicted_doublets: 1 unique values
      - leiden: 55 unique values
      - UMAP_X: 20655 unique values
      ... and 607 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (46394, 2)
   X range: [-4.49, 20.55]
   Y range: [-6.76, 14.99]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP121
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP121/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP121/SP121.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 1,245,413 cells × 19,739 genes
   📋 obs columns: 35
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 339 unique values
      - Tissue: 40 unique values
      - n_genes_by_counts: 5800 unique values
      - total_counts: 41524 unique values
      - total_counts_mt: 4924 unique values
      - pct_counts_mt: 934556 unique values
      - n_genes: 5800 unique values
      - FolderID: 54 unique values
      - LatinName: 1 unique values
      - Region: 9 unique values
      ... and 25 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (1245413, 2)
   X range: [-6.79, 27.55]
   Y range: [-9.70, 28.35]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 108
   Mapped unique types: 108

   Sample mappings:
      "Inflammatory Chondrocytes" → "Inflammatory chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"
      "Effector Chondrocytes" → "Effector chondrocytes"
      "Hypertrophic Chondrocytes" → "Hypertrophic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             15    176,762
   Immune cells             20    581,269
   Epithelial cells         38    147,936
   Stromal cells            20    213,584
   Muscle cells              6     43,282
   Germ cells                2      5,621
   Endothelial cells         1     74,078
   Other                     6      2,881
   Other                     6      2,881
   ────────────────────────────────────────
   TOTAL                   108  1,245,413

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/umap.bin.gz (gzip compressed)...
   ✅ 1,245,413 cells × 10 bytes
   📦 Uncompressed: 11.88 MB
   📦 Compressed:   9.23 MB (22.3% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/umap_meta.json ...
   ✅ 16.9 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP121/celltype_legend.json ...
   ✅ 20.8 KB

🔍 Verification (first 3 cells):
   Cell 0: (   12.56,    24.65) idx= 22 "Macrophages" ✅
   Cell 1: (   12.13,    23.82) idx= 22 "Macrophages" ✅
   Cell 2: (    8.00,    26.98) idx= 32 "T_NKT cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 40 tissues
      - Lymph node: 130,970 cells
      - Adipose: 87,144 cells
      - Blood: 82,242 cells
      - cerebral cortex: 79,664 cells
      - Spleen: 68,456 cells
      ... and 35 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP121/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 1,245,413 cells × 19,739 genes

💾 gene_list.json: 19,739 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 19,739 genes

   📊 Summary:
      gene_list.json   : 183.2 KB
      genes/*.bin.gz   : 1 files, 158.5 KB total
      Uncompressed     : ~4864.9 KB
      Compression      : 96.7% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP121/

📄 Generated files:
   SP121/
   ├── umap.bin.gz           (9.23 MB)
   ├── umap_meta.json        (16.9 KB)
   ├── celltype_legend.json  (20.8 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (183.2 KB, 19,739 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP121
   • Total cells:       1,245,413
   • Cell types:              108
   • Genes (total):        19,739
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 19,739 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP121


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP123
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP123/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP123/SP123.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 28,099 cells × 3,000 genes
   📋 obs columns: 611
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 19 unique values
      - Tissue: 2 unique values
      - Region: 2 unique values
      - DevoStage: 1 unique values
      - CellType: 9 unique values
      - n_genes: 5126 unique values
      - doublet_scores: 316 unique values
      - predicted_doublets: 1 unique values
      - leiden: 39 unique values
      - UMAP_X: 28083 unique values
      ... and 601 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (28099, 2)
   X range: [-4.49, 21.89]
   Y range: [-10.21, 18.19]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP124
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP124/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP124/SP124.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 525,763 cells × 16,867 genes
   📋 obs columns: 36
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 309 unique values
      - Tissue: 25 unique values
      - Region: 5 unique values
      - BrainRegion: 8 unique values
      - DevoStage: 1 unique values
      - Timing: 8 unique values
      - n_genes_by_counts: 5619 unique values
      - total_counts: 69042 unique values
      - total_counts_mt: 1756 unique values
      - pct_counts_mt: 382500 unique values
      ... and 26 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (525763, 2)
   X range: [-12.68, 20.72]
   Y range: [-14.54, 18.34]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 83
   Mapped unique types: 83

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             16    434,954
   Immune cells             21     39,854
   Epithelial cells         26     21,827
   Stromal cells             8     15,008
   Muscle cells              4      1,676
   Germ cells                2      1,246
   Endothelial cells         1     10,004
   Other                     5      1,194
   Other                     5      1,194
   ────────────────────────────────────────
   TOTAL                    83    525,763

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/umap.bin.gz (gzip compressed)...
   ✅ 525,763 cells × 10 bytes
   📦 Uncompressed: 5.01 MB
   📦 Compressed:   3.87 MB (22.9% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/umap_meta.json ...
   ✅ 13.2 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP124/celltype_legend.json ...
   ✅ 16.2 KB

🔍 Verification (first 3 cells):
   Cell 0: (   11.88,    10.36) idx=  8 "Inhibitory neurons" ✅
   Cell 1: (   11.76,    10.66) idx=  8 "Inhibitory neurons" ✅
   Cell 2: (   11.68,    10.16) idx=  8 "Inhibitory neurons" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 25 tissues
      - Brain: 440,947 cells
      - Spleen: 11,252 cells
      - Tongue: 8,834 cells
      - Marrow: 8,503 cells
      - Retina: 7,682 cells
      ... and 20 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP124/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 525,763 cells × 16,867 genes

💾 gene_list.json: 16,867 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,867 genes

   📊 Summary:
      gene_list.json   : 154.4 KB
      genes/*.bin.gz   : 1 files, 9.5 KB total
      Uncompressed     : ~2053.8 KB
      Compression      : 99.5% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP124/

📄 Generated files:
   SP124/
   ├── umap.bin.gz           (3.87 MB)
   ├── umap_meta.json        (13.2 KB)
   ├── celltype_legend.json  (16.2 KB)
   ├── tissue_info.json      (1.5 KB)
   ├── config.json
   ├── gene_list.json        (154.4 KB, 16,867 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP124
   • Total cells:         525,763
   • Cell types:               83
   • Genes (total):        16,867
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,867 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP124


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP126
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP126/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP126/SP126.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 483,358 cells × 16,460 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 0 unique values
      - Tissue: 15 unique values
      - n_genes: 5493 unique values
      - FolderID: 16 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 54 unique values
      - celltypist_over_clustering: 595 unique values
      - celltypist_majority_voting: 41 unique values
      - leiden_res1.0: 402 unique values
      - deepseek_v3.2_celltype: 81 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (483358, 2)
   X range: [-8.53, 28.46]
   Y range: [-10.61, 22.16]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 59
   Mapped unique types: 59

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             12     15,322
   Immune cells             15    104,107
   Epithelial cells         15     14,763
   Stromal cells             6    170,931
   Muscle cells              4     96,388
   Germ cells                2      1,763
   Endothelial cells         1     79,407
   Other                     4        677
   Other                     4        677
   ────────────────────────────────────────
   TOTAL                    59    483,358

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/umap.bin.gz (gzip compressed)...
   ✅ 483,358 cells × 10 bytes
   📦 Uncompressed: 4.61 MB
   📦 Compressed:   3.72 MB (19.3% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/umap_meta.json ...
   ✅ 9.7 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP126/celltype_legend.json ...
   ✅ 11.9 KB

🔍 Verification (first 3 cells):
   Cell 0: (   27.07,     3.04) idx= 50 "Smooth muscle cells" ✅
   Cell 1: (   24.29,     6.25) idx= 17 "Macrophages" ✅
   Cell 2: (   26.07,     6.63) idx= 47 "Stromal cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 15 tissues
      - Heart: 327,313 cells
      - Aorta: 43,752 cells
      - Spleen: 14,659 cells
      - PBMC: 12,826 cells
      - WAT: 12,391 cells
      ... and 10 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP126/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 483,358 cells × 16,460 genes

💾 gene_list.json: 16,460 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,460 genes

   📊 Summary:
      gene_list.json   : 150.2 KB
      genes/*.bin.gz   : 1 files, 6.8 KB total
      Uncompressed     : ~1888.1 KB
      Compression      : 99.6% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP126/

📄 Generated files:
   SP126/
   ├── umap.bin.gz           (3.72 MB)
   ├── umap_meta.json        (9.7 KB)
   ├── celltype_legend.json  (11.9 KB)
   ├── tissue_info.json      (0.9 KB)
   ├── config.json
   ├── gene_list.json        (150.2 KB, 16,460 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP126
   • Total cells:         483,358
   • Cell types:               59
   • Genes (total):        16,460
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,460 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP126


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP129
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP129/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP129/SP129.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,642 cells × 3,000 genes
   📋 obs columns: 544
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 1 unique values
      - Tissue: 1 unique values
      - Region: 2 unique values
      - DevoStage: 1 unique values
      - CellType: 1 unique values
      - n_genes: 4018 unique values
      - doublet_scores: 170 unique values
      - predicted_doublets: 1 unique values
      - leiden: 21 unique values
      - UMAP_X: 16639 unique values
      ... and 534 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16642, 2)
   X range: [-8.79, 16.05]
   Y range: [-5.15, 20.58]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP130
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP130/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP130/SP130.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,931 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 10 unique values
      - CellType: 6 unique values
      - n_genes: 3582 unique values
      - doublet_scores: 231 unique values
      - predicted_doublets: 1 unique values
      - leiden: 35 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16931, 2)
   X range: [-10.84, 14.24]
   Y range: [-6.85, 19.30]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1479
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1479/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1479/SP1479.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 19,999 cells × 3,000 genes
   📋 obs columns: 617
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 9538 unique values
      - nFeature_RNA: 3617 unique values
      - percent.mt: 1 unique values
      - Tissue: 2 unique values
      - integrated_snn_res.0.6: 27 unique values
      - seurat_clusters: 27 unique values
      - day: 4 unique values
      - day_condition: 8 unique values
      - Genotype: 3 unique values
      ... and 607 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (19999, 2)
   X range: [-6.39, 16.65]
   Y range: [-9.05, 14.31]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1568
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1568/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1568/SP1568.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 80,658 cells × 13,456 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 51 unique values
      - Tissue: 7 unique values
      - n_genes: 2008 unique values
      - FolderID: 7 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 37 unique values
      - celltypist_over_clustering: 382 unique values
      - celltypist_majority_voting: 26 unique values
      - leiden_res1.0: 89 unique values
      - deepseek_v3.2_celltype: 44 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (80658, 2)
   X range: [-5.59, 16.93]
   Y range: [-11.44, 18.74]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 34
   Mapped unique types: 34

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells              7     16,018
   Immune cells              7     12,525
   Epithelial cells         13     30,303
   Stromal cells             3      8,669
   Muscle cells              2      7,653
   Germ cells                1        260
   Endothelial cells         1      5,230
   ────────────────────────────────────────
   TOTAL                    34     80,658

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP1568/umap.bin.gz (gzip compressed)...
   ✅ 80,658 cells × 10 bytes
   📦 Uncompressed: 0.77 MB
   📦 Compressed:   0.61 MB (20.7% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP1568/umap_meta.json ...
   ✅ 6.0 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP1568/celltype_legend.json ...
   ✅ 6.7 KB

🔍 Verification (first 3 cells):
   Cell 0: (    6.26,    -1.14) idx=  4 "Inhibitory neurons" ✅
   Cell 1: (    5.28,    -2.83) idx=  4 "Inhibitory neurons" ✅
   Cell 2: (    9.27,    -2.00) idx=  4 "Inhibitory neurons" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 7 tissues
      - Liver: 22,049 cells
      - Brain: 16,094 cells
      - Heart: 15,650 cells
      - Spleen: 11,445 cells
      - Kidney: 9,194 cells
      ... and 2 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP1568/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 80,658 cells × 13,456 genes

💾 gene_list.json: 13,456 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 13,456 genes

   📊 Summary:
      gene_list.json   : 122.0 KB
      genes/*.bin.gz   : 1 files, 15.5 KB total
      Uncompressed     : ~315.1 KB
      Compression      : 95.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1568/

📄 Generated files:
   SP1568/
   ├── umap.bin.gz           (0.61 MB)
   ├── umap_meta.json        (6.0 KB)
   ├── celltype_legend.json  (6.7 KB)
   ├── tissue_info.json      (0.5 KB)
   ├── config.json
   ├── gene_list.json        (122.0 KB, 13,456 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP1568
   • Total cells:          80,658
   • Cell types:               34
   • Genes (total):        13,456
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 13,456 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP1568


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1572
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1572/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1572/SP1572.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,283 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 3373 unique values
      - doublet_scores: 174 unique values
      - predicted_doublets: 1 unique values
      - leiden: 39 unique values
      - UMAP_X: 15281 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15283, 2)
   X range: [-8.40, 18.12]
   Y range: [-8.53, 21.40]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1755
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1755/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1755/SP1755.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,078 cells × 3,000 genes
   📋 obs columns: 580
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 13078 unique values
      - nFeature_RNA: 2091 unique values
      - tissue: 2 unique values
      - batch: 12 unique values
      - Org_celltype: 29 unique values
      - cellname: 33 unique values
      - stage: 0 unique values
      - subtype: 51 unique values
      - species: 1 unique values
      ... and 570 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13078, 2)
   X range: [-3.08, 14.78]
   Y range: [-5.45, 12.63]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1780
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1780/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1780/SP1780.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,589 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 3378 unique values
      - doublet_scores: 219 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13589, 2)
   X range: [-6.85, 20.67]
   Y range: [-11.06, 15.95]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1784
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1784/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1784/SP1784.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 33,383 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 7 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 7 unique values
      - n_genes: 2522 unique values
      - doublet_scores: 254 unique values
      - predicted_doublets: 1 unique values
      - leiden: 38 unique values
      - UMAP_X: 33371 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (33383, 2)
   X range: [-4.27, 23.83]
   Y range: [-6.30, 20.94]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1793
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1793/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1793/SP1793.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 32,921 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 5128 unique values
      - doublet_scores: 246 unique values
      - predicted_doublets: 1 unique values
      - leiden: 38 unique values
      - UMAP_X: 32912 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (32921, 2)
   X range: [-10.81, 16.58]
   Y range: [-13.53, 16.50]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1796
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1796/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1796/SP1796.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 14,274 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 4763 unique values
      - doublet_scores: 168 unique values
      - predicted_doublets: 1 unique values
      - leiden: 35 unique values
      - UMAP_X: 14269 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (14274, 2)
   X range: [-9.37, 17.83]
   Y range: [-14.51, 15.20]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1799
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1799/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1799/SP1799.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 111,538 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - n_genes: 5591 unique values
      - doublet_scores: 459 unique values
      - predicted_doublets: 1 unique values
      - leiden: 38 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (111538, 2)
   X range: [-10.87, 19.12]
   Y range: [-6.09, 22.46]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1800
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1800/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1800/SP1800.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 25,225 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 8 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 8 unique values
      - n_genes: 4838 unique values
      - doublet_scores: 215 unique values
      - predicted_doublets: 1 unique values
      - leiden: 32 unique values
      - UMAP_X: 25209 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (25225, 2)
   X range: [-8.99, 20.80]
   Y range: [-7.80, 15.47]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1804
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1804/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1804/SP1804.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 24,672 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 2179 unique values
      - doublet_scores: 278 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (24672, 2)
   X range: [-3.36, 22.69]
   Y range: [-6.73, 18.72]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP1823
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP1823/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP1823/SP1823.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 44,328 cells × 3,000 genes
   📋 obs columns: 19
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 0 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - n_genes: 3416 unique values
      - doublet_scores: 286 unique values
      - predicted_doublets: 1 unique values
      - leiden: 22 unique values
      - UMAP_X: 44289 unique values
      - UMAP_Y: 44311 unique values
      ... and 9 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (44328, 2)
   X range: [-7.00, 17.94]
   Y range: [-8.58, 19.85]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP189
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP189/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP189/SP189.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 23,645 cells × 3,000 genes
   📋 obs columns: 616
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 659 unique values
      - nFeature_RNA: 580 unique values
      - integrated_snn_res.1: 38 unique values
      - seurat_clusters: 38 unique values
      - Org_celltype: 16 unique values
      - Tissue: 2 unique values
      - LatinName: 1 unique values
      - n_genes: 3069 unique values
      - doublet_scores: 333 unique values
      ... and 606 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (23645, 2)
   X range: [-4.29, 18.61]
   Y range: [-8.49, 16.35]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP191
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP191/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP191/SP191.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,957 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 6 unique values
      - n_genes: 2333 unique values
      - doublet_scores: 232 unique values
      - predicted_doublets: 1 unique values
      - leiden: 29 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16957, 2)
   X range: [-6.88, 15.42]
   Y range: [-5.57, 20.02]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP194
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP194/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP194/SP194.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,489 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2351 unique values
      - doublet_scores: 213 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13489, 2)
   X range: [-6.57, 16.03]
   Y range: [-3.36, 20.44]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP197
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP197/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP197/SP197.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 94,738 cells × 3,000 genes
   📋 obs columns: 579
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 2 unique values
      - nCount_RNA: 7375 unique values
      - nFeature_RNA: 4246 unique values
      - orig.file: 2 unique values
      - RNA_snn_res.0.5: 34 unique values
      - seurat_clusters: 34 unique values
      - dendro_order: 34 unique values
      - Org_celltype: 14 unique values
      - Tissue: 2 unique values
      - LatinName: 1 unique values
      ... and 569 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (94738, 2)
   X range: [-11.68, 15.38]
   Y range: [-5.54, 19.25]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP198
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP198/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP198/SP198.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 6,692 cells × 3,000 genes
   📋 obs columns: 608
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - CELL: 6692 unique values
      - Species: 1 unique values
      - UMAP1: 6690 unique values
      - UMAP2: 6691 unique values
      - Org_celltype: 5 unique values
      - nUMI: 2799 unique values
      - Pseudotime: 6428 unique values
      - X_Y_classification: 4 unique values
      - Tissue: 1 unique values
      - LatinName: 1 unique values
      ... and 598 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (6692, 2)
   X range: [0.74, 19.20]
   Y range: [-5.79, 9.38]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP199
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP199/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP199/SP199.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 6,552 cells × 3,000 genes
   📋 obs columns: 609
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - UMAP1: 6552 unique values
      - UMAP2: 6552 unique values
      - Org_celltype: 10 unique values
      - nUMI: 2663 unique values
      - Pseudotime: 4934 unique values
      - X_Y_classification: 0 unique values
      - Tissue: 1 unique values
      - n_genes: 3131 unique values
      - doublet_scores: 105 unique values
      - predicted_doublets: 1 unique values
      ... and 599 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (6552, 2)
   X range: [-8.88, 18.52]
   Y range: [-5.35, 15.62]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP200
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP200/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP200/SP200.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 226,929 cells × 3,000 genes
   📋 obs columns: 623
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 19 unique values
      - Tissue: 2 unique values
      - Region: 2 unique values
      - DevoStage: 1 unique values
      - CellType: 9 unique values
      - n_genes: 5782 unique values
      - doublet_scores: 1217 unique values
      - predicted_doublets: 1 unique values
      - leiden: 54 unique values
      - UMAP_X: 226411 unique values
      ... and 613 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (226929, 2)
   X range: [-4.26, 20.69]
   Y range: [-8.42, 19.26]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP201
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP201/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP201/SP201.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,004 cells × 3,000 genes
   📋 obs columns: 594
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Timing: 10 unique values
      - Org_celltype: 8 unique values
      - CellType: 8 unique values
      - n_genes: 2427 unique values
      - doublet_scores: 518 unique values
      - predicted_doublets: 1 unique values
      - leiden: 17 unique values
      ... and 584 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10004, 2)
   X range: [-2.42, 15.43]
   Y range: [-7.37, 8.73]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP202
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP202/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP202/SP202.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 796,851 cells × 16,423 genes
   📋 obs columns: 38
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 82 unique values
      - SpecieID: 2 unique values
      - RegionID: 41 unique values
      - Double_score: 45978 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5795 unique values
      - total_counts: 24949 unique values
      - total_counts_mt: 2450 unique values
      - pct_counts_mt: 268525 unique values
      - n_genes: 5795 unique values
      ... and 28 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (796851, 2)
   X range: [-10.00, 22.44]
   Y range: [-7.83, 24.33]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 114
   Mapped unique types: 114

   Sample mappings:
      "Fibrocartilage Chondrocytes" → "Fibrocartilage chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             17    239,944
   Immune cells             24    202,999
   Epithelial cells         42    140,326
   Stromal cells            14     92,961
   Muscle cells              7     59,072
   Germ cells                2     18,820
   Endothelial cells         1     39,893
   Other                     7      2,836
   Other                     7      2,836
   ────────────────────────────────────────
   TOTAL                   114    796,851

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP202/umap.bin.gz (gzip compressed)...
   ✅ 796,851 cells × 10 bytes
   📦 Uncompressed: 7.60 MB
   📦 Compressed:   5.87 MB (22.7% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP202/umap_meta.json ...
   ✅ 17.7 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP202/celltype_legend.json ...
   ✅ 21.9 KB

🔍 Verification (first 3 cells):
   Cell 0: (    9.24,     8.89) idx= 78 "Serous cells" ✅
   Cell 1: (    9.05,     8.70) idx= 78 "Serous cells" ✅
   Cell 2: (    9.14,     9.25) idx= 78 "Serous cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 38 tissues
      - Neocortex: 106,200 cells
      - Testes: 27,072 cells
      - Hypothalamus: 25,336 cells
      - Striatum: 23,789 cells
      - Thyroid: 23,678 cells
      ... and 33 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP202/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 796,851 cells × 16,423 genes

💾 gene_list.json: 16,423 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,423 genes

   📊 Summary:
      gene_list.json   : 150.0 KB
      genes/*.bin.gz   : 1 files, 67.4 KB total
      Uncompressed     : ~3112.7 KB
      Compression      : 97.8% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP202/

📄 Generated files:
   SP202/
   ├── umap.bin.gz           (5.87 MB)
   ├── umap_meta.json        (17.7 KB)
   ├── celltype_legend.json  (21.9 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (150.0 KB, 16,423 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP202
   • Total cells:         796,851
   • Cell types:              114
   • Genes (total):        16,423
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,423 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP202


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP2036
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP2036/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP2036/SP2036.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 9,999 cells × 3,000 genes
   📋 obs columns: 605
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 7 unique values
      - nCount_RNA: 3380 unique values
      - nFeature_RNA: 2320 unique values
      - orig.file: 7 unique values
      - RNA_snn_res.0.5: 35 unique values
      - seurat_clusters: 35 unique values
      - dendro_order: 35 unique values
      - Org_celltype: 9 unique values
      - source_file: 1 unique values
      - batch: 1 unique values
      ... and 595 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (9999, 2)
   X range: [-9.80, 24.52]
   Y range: [-14.52, 25.18]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP2038
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP2038/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP2038/SP2038.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,000 cells × 3,000 genes
   📋 obs columns: 606
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 6 unique values
      - nCount_RNA: 2078 unique values
      - nFeature_RNA: 1500 unique values
      - orig.file: 6 unique values
      - RNA_snn_res.0.5: 27 unique values
      - seurat_clusters: 27 unique values
      - dendro_order: 27 unique values
      - Org_celltype: 9 unique values
      - Tissue: 1 unique values
      - LatinName: 1 unique values
      ... and 596 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10000, 2)
   X range: [1.66, 16.36]
   Y range: [-1.74, 10.03]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP214
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP214/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP214/SP214.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 6,487 cells × 3,000 genes
   📋 obs columns: 20
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 1 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - CellType: 1 unique values
      - n_genes: 1405 unique values
      - doublet_scores: 97 unique values
      - predicted_doublets: 1 unique values
      - leiden: 7 unique values
      - UMAP_X: 6487 unique values
      ... and 10 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (6487, 2)
   X range: [-4.29, 7.30]
   Y range: [-0.48, 7.84]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP215
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP215/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP215/SP215.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 17,452 cells × 3,001 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 2953 unique values
      - doublet_scores: 234 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (17452, 2)
   X range: [-10.55, 15.22]
   Y range: [-9.34, 13.98]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP2213
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP2213/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP2213/SP2213.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 573,449 cells × 17,308 genes
   📋 obs columns: 38
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 82 unique values
      - SpecieID: 1 unique values
      - RegionID: 44 unique values
      - Double_score: 37355 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5798 unique values
      - total_counts: 24258 unique values
      - total_counts_mt: 2806 unique values
      - pct_counts_mt: 274914 unique values
      - n_genes: 5798 unique values
      ... and 28 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (573449, 2)
   X range: [-13.62, 21.06]
   Y range: [-9.45, 24.81]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 117
   Mapped unique types: 117

   Sample mappings:
      "Fibrocartilage Chondrocytes" → "Fibrocartilage chondrocytes"
      "Inflammatory Chondrocytes" → "Inflammatory chondrocytes"
      "Homeostatic Chondrocytes" → "Homeostatic chondrocytes"

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             22    144,213
   Immune cells             19    149,032
   Epithelial cells         41    113,775
   Stromal cells            17     85,290
   Muscle cells              7     58,268
   Germ cells                3        775
   Endothelial cells         1     20,034
   Other                     7      2,062
   Other                     7      2,062
   ────────────────────────────────────────
   TOTAL                   117    573,449

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP2213/umap.bin.gz (gzip compressed)...
   ✅ 573,449 cells × 10 bytes
   📦 Uncompressed: 5.47 MB
   📦 Compressed:   4.21 MB (23.1% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP2213/umap_meta.json ...
   ✅ 18.2 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP2213/celltype_legend.json ...
   ✅ 22.4 KB

🔍 Verification (first 3 cells):
   Cell 0: (   10.64,    -2.28) idx= 62 "Hepatocytes" ✅
   Cell 1: (   10.53,    -2.27) idx= 62 "Hepatocytes" ✅
   Cell 2: (   10.73,    -1.79) idx= 62 "Hepatocytes" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 38 tissues
      - Neocortex: 79,144 cells
      - Hippocampus: 22,651 cells
      - Tonsil: 21,973 cells
      - Kidney: 20,990 cells
      - Sciatic nerve: 20,795 cells
      ... and 33 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP2213/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 573,449 cells × 17,308 genes

💾 gene_list.json: 17,308 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 17,308 genes

   📊 Summary:
      gene_list.json   : 158.6 KB
      genes/*.bin.gz   : 1 files, 49.9 KB total
      Uncompressed     : ~2240.0 KB
      Compression      : 97.8% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP2213/

📄 Generated files:
   SP2213/
   ├── umap.bin.gz           (4.21 MB)
   ├── umap_meta.json        (18.2 KB)
   ├── celltype_legend.json  (22.4 KB)
   ├── tissue_info.json      (2.4 KB)
   ├── config.json
   ├── gene_list.json        (158.6 KB, 17,308 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP2213
   • Total cells:         573,449
   • Cell types:              117
   • Genes (total):        17,308
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 17,308 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP2213


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP239
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP239/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP239/SP239.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 661,961 cells × 15,892 genes
   📋 obs columns: 32
   🗺️  obsm keys: ['X_pca', 'X_umap', 'X_umap_bbknn']

   Sample obs columns:
      - Tissue: 18 unique values
      - Double_score: 26928 unique values
      - Double_result: 1 unique values
      - n_genes_by_counts: 5791 unique values
      - total_counts: 27847 unique values
      - total_counts_mt: 3112 unique values
      - pct_counts_mt: 274580 unique values
      - n_genes: 5791 unique values
      - leiden_0.5: 46 unique values
      - leiden_1.0: 66 unique values
      ... and 22 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (661961, 2)
   X range: [-8.75, 24.16]
   Y range: [-12.90, 20.71]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP244
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP244/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP244/SP244.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 139,347 cells × 3,000 genes
   📋 obs columns: 609
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 8 unique values
      - nCount_RNA: 6179 unique values
      - nFeature_RNA: 3518 unique values
      - orig.file: 8 unique values
      - RNA_snn_res.0.5: 81 unique values
      - seurat_clusters: 66 unique values
      - RNA_snn_res.0.2: 66 unique values
      - dendro_order: 66 unique values
      - Org_celltype: 14 unique values
      - Tissue: 2 unique values
      ... and 599 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (139347, 2)
   X range: [-13.81, 12.44]
   Y range: [-13.70, 12.03]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP301
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP301/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP301/SP301.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 227,879 cells × 14,862 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 142 unique values
      - Tissue: 26 unique values
      - n_genes: 5354 unique values
      - FolderID: 26 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 71 unique values
      - celltypist_over_clustering: 217 unique values
      - celltypist_majority_voting: 56 unique values
      - leiden_res1.0: 565 unique values
      - deepseek_v3.2_celltype: 108 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (227879, 2)
   X range: [-6.94, 24.60]
   Y range: [-11.36, 24.46]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 72
   Mapped unique types: 72

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             11      2,991
   Immune cells             17    148,751
   Epithelial cells         25     42,431
   Stromal cells             5     12,529
   Muscle cells              4      1,187
   Germ cells                2      5,567
   Endothelial cells         1     13,188
   Other                     7      1,235
   Other                     7      1,235
   ────────────────────────────────────────
   TOTAL                    72    227,879

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP301/umap.bin.gz (gzip compressed)...
   ✅ 227,879 cells × 10 bytes
   📦 Uncompressed: 2.17 MB
   📦 Compressed:   1.71 MB (21.4% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP301/umap_meta.json ...
   ✅ 11.5 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP301/celltype_legend.json ...
   ✅ 14.5 KB

🔍 Verification (first 3 cells):
   Cell 0: (   19.54,    11.58) idx= 26 "T cells" ✅
   Cell 1: (   17.41,    15.68) idx= 24 "Plasma B cells" ✅
   Cell 2: (   23.64,    12.97) idx= 11 "B cells" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 26 tissues
      - Bone marrow: 34,521 cells
      - Lung: 33,054 cells
      - Skin: 24,652 cells
      - Blood: 21,476 cells
      - Bone: 14,846 cells
      ... and 21 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP301/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 227,879 cells × 14,862 genes

💾 gene_list.json: 14,862 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 14,862 genes

   📊 Summary:
      gene_list.json   : 135.1 KB
      genes/*.bin.gz   : 1 files, 7.2 KB total
      Uncompressed     : ~890.2 KB
      Compression      : 99.2% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP301/

📄 Generated files:
   SP301/
   ├── umap.bin.gz           (1.71 MB)
   ├── umap_meta.json        (11.5 KB)
   ├── celltype_legend.json  (14.5 KB)
   ├── tissue_info.json      (1.6 KB)
   ├── config.json
   ├── gene_list.json        (135.1 KB, 14,862 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP301
   • Total cells:         227,879
   • Cell types:               72
   • Genes (total):        14,862
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 14,862 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP301


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP308
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP308/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP308/SP308.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 143,349 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - n_genes: 5580 unique values
      - doublet_scores: 535 unique values
      - predicted_doublets: 1 unique values
      - leiden: 39 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (143349, 2)
   X range: [-4.71, 23.39]
   Y range: [-11.59, 19.70]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP309
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP309/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP309/SP309.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 91,355 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 4 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 6 unique values
      - CellType: 4 unique values
      - n_genes: 5515 unique values
      - doublet_scores: 410 unique values
      - predicted_doublets: 1 unique values
      - leiden: 34 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (91355, 2)
   X range: [-9.06, 17.11]
   Y range: [-9.34, 17.97]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP310
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP310/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP310/SP310.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 125,593 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 6 unique values
      - n_genes: 5593 unique values
      - doublet_scores: 484 unique values
      - predicted_doublets: 1 unique values
      - leiden: 36 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (125593, 2)
   X range: [-12.53, 16.06]
   Y range: [-7.55, 22.58]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP311
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP311/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP311/SP311.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 71,060 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - n_genes: 5572 unique values
      - doublet_scores: 361 unique values
      - predicted_doublets: 1 unique values
      - leiden: 41 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (71060, 2)
   X range: [-9.99, 20.36]
   Y range: [-10.38, 18.74]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP317
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP317/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP317/SP317.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 114,450 cells × 3,000 genes
   📋 obs columns: 10
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 6 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - Org_celltype: 6 unique values
      - Region: 2 unique values
      - Tissue: 1 unique values
      - _index: 114450 unique values
      - doublet_scores: 700 unique values
      - n_genes: 5739 unique values
      - predicted_doublets: 1 unique values

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP318
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP318/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP318/SP318.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 47,994 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - n_genes: 5555 unique values
      - doublet_scores: 302 unique values
      - predicted_doublets: 1 unique values
      - leiden: 32 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (47994, 2)
   X range: [-5.49, 23.34]
   Y range: [-7.13, 24.34]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP327
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP327/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP327/SP327.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 8,305 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 3 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 4 unique values
      - Anno_Fish: 5 unique values
      - CellType: 3 unique values
      - n_genes: 2958 unique values
      - doublet_scores: 121 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (8305, 2)
   X range: [-4.22, 26.36]
   Y range: [-5.11, 21.81]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP373
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP373/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP373/SP373.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 17,828 cells × 3,001 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 3564 unique values
      - doublet_scores: 230 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (17828, 2)
   X range: [-6.71, 16.49]
   Y range: [-3.49, 20.06]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP374
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP374/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP374/SP374.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,484 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2800 unique values
      - doublet_scores: 238 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15484, 2)
   X range: [-2.89, 20.75]
   Y range: [-4.15, 21.08]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP375
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP375/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP375/SP375.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 14,176 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2313 unique values
      - doublet_scores: 217 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (14176, 2)
   X range: [-10.18, 14.76]
   Y range: [-5.83, 20.74]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP376
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP376/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP376/SP376.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 27,686 cells × 3,000 genes
   📋 obs columns: 602
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 1 unique values
      - nCount_RNA: 1079 unique values
      - nFeature_RNA: 897 unique values
      - RNA_snn_res.0.2: 6 unique values
      - seurat_clusters: 40 unique values
      - integrated_snn_res.1: 40 unique values
      - Org_celltype: 16 unique values
      - Tissue: 2 unique values
      - LatinName: 1 unique values
      - n_genes: 3943 unique values
      ... and 592 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (27686, 2)
   X range: [-5.28, 18.63]
   Y range: [-4.52, 21.42]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP389
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP389/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP389/SP389.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,832 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 2 unique values
      - n_genes: 2112 unique values
      - doublet_scores: 239 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16832, 2)
   X range: [-0.40, 19.02]
   Y range: [-2.81, 12.69]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP406
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP406/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP406/SP406.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,368 cells × 1,936 genes
   📋 obs columns: 9
   🗺️  obsm keys: []

   Sample obs columns:
      - CellType: 9 unique values
      - DevoStage: 1 unique values
      - Org_celltype: 9 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 19299 unique values
      - doublet_scores: 441 unique values
      - n_genes: 4337 unique values
      - predicted_doublets: 1 unique values

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP421
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP421/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP421/SP421.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 19,579 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 5 unique values
      - n_genes: 3491 unique values
      - doublet_scores: 267 unique values
      - predicted_doublets: 1 unique values
      - leiden: 39 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (19579, 2)
   X range: [-3.86, 24.21]
   Y range: [-9.06, 20.17]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP429
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP429/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP429/SP429.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 20,308 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 6 unique values
      - n_genes: 2396 unique values
      - doublet_scores: 134 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (20308, 2)
   X range: [-7.27, 17.04]
   Y range: [-5.06, 18.33]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP438
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP438/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP438/SP438.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,001 cells × 3,000 genes
   📋 obs columns: 602
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 6 unique values
      - CellType: 5 unique values
      - Anno_Human: 4 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 1414 unique values
      - doublet_scores: 142 unique values
      ... and 592 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10001, 2)
   X range: [-4.53, 12.55]
   Y range: [-3.02, 13.49]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP447
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP447/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP447/SP447.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,480 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2851 unique values
      - doublet_scores: 230 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15480, 2)
   X range: [-3.28, 21.61]
   Y range: [-10.74, 16.82]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP451
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP451/SP451.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 275,033 cells × 16,999 genes
   📋 obs columns: 16
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 84 unique values
      - Tissue: 20 unique values
      - n_genes: 3810 unique values
      - FolderID: 20 unique values
      - LatinName: 1 unique values
      - celltypist_predicted_labels: 62 unique values
      - celltypist_over_clustering: 411 unique values
      - celltypist_majority_voting: 48 unique values
      - leiden_res1.0: 454 unique values
      - deepseek_v3.2_celltype: 111 unique values
      ... and 6 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (275033, 2)
   X range: [-8.80, 24.33]
   Y range: [-13.03, 23.83]

🏷️  Cell type column: "laca_curated_celltype_v3"
   Raw unique types: 72
   Mapped unique types: 72

🎨 Building cell type metadata...

   Category              Types      Cells
   ────────────────────────────────────────
   Neural cells             18     37,718
   Immune cells             16     75,104
   Epithelial cells         23     83,935
   Stromal cells             6     34,550
   Muscle cells              3      4,144
   Germ cells                2        706
   Endothelial cells         1     35,951
   Other                     3      2,925
   Other                     3      2,925
   ────────────────────────────────────────
   TOTAL                    72    275,033

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/umap.bin.gz (gzip compressed)...
   ✅ 275,033 cells × 10 bytes
   📦 Uncompressed: 2.62 MB
   📦 Compressed:   2.10 MB (19.9% reduction)

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/umap_meta.json ...
   ✅ 11.6 KB

💾 Writing /mnt/alamo01/projects/test_20241129/cds_test/SP451/celltype_legend.json ...
   ✅ 14.0 KB

🔍 Verification (first 3 cells):
   Cell 0: (   18.75,     8.87) idx=  5 "Inhibitory neurons" ✅
   Cell 1: (   19.73,    12.51) idx=  5 "Inhibitory neurons" ✅
   Cell 2: (   21.26,    13.27) idx= 25 "Microglia" ✅

======================================================================
🫁 Generating tissue information
======================================================================
   Tissue column: "Tissue"
   ✅ Found 20 tissues
      - Kidney: 43,236 cells
      - Pancreas: 37,908 cells
      - Pituitary gland: 23,598 cells
      - Muscle: 21,004 cells
      - Cerebellum: 16,017 cells
      ... and 15 more
   💾 /mnt/alamo01/projects/test_20241129/cds_test/SP451/tissue_info.json

======================================================================
🧬 Generating gene expression data files
======================================================================

   Matrix type: sparse
   Matrix shape: 275,033 cells × 16,999 genes

💾 gene_list.json: 16,999 genes

📦 Exporting only the FIRST gene: "A1BG" (gzip compressed)
   💡 Use --all-genes to export all 16,999 genes

   📊 Summary:
      gene_list.json   : 155.4 KB
      genes/*.bin.gz   : 1 files, 63.5 KB total
      Uncompressed     : ~1074.3 KB
      Compression      : 94.1% reduction

══════════════════════════════════════════════════════════════════════
  🎉 Generation Complete!
══════════════════════════════════════════════════════════════════════

📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP451/

📄 Generated files:
   SP451/
   ├── umap.bin.gz           (2.10 MB)
   ├── umap_meta.json        (11.6 KB)
   ├── celltype_legend.json  (14.0 KB)
   ├── tissue_info.json      (1.2 KB)
   ├── config.json
   ├── gene_list.json        (155.4 KB, 16,999 genes)
   └── genes/
       └── A1BG.bin.gz  (only first gene)

📊 Statistics:
   • SP_ID:            SP451
   • Total cells:         275,033
   • Cell types:               72
   • Genes (total):        16,999
   • Genes (exported):          1

💡 Tip: Run with --all-genes to export all 16,999 gene files

🌐 Access URL: speciesinfo.php?SP_ID=SP451


══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP452
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP452/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP452/SP452.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,552 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 3103 unique values
      - doublet_scores: 205 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13552, 2)
   X range: [-8.93, 11.67]
   Y range: [-10.67, 15.72]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP454
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP454/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP454/SP454.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 18,771 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2637 unique values
      - doublet_scores: 239 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (18771, 2)
   X range: [-5.66, 17.92]
   Y range: [-9.74, 14.61]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP459
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP459/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP459/SP459.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 14,377 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 3 unique values
      - n_genes: 2836 unique values
      - doublet_scores: 224 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (14377, 2)
   X range: [-5.12, 22.46]
   Y range: [-7.92, 19.55]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP460
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP460/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP460/SP460.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 8,891 cells × 3,000 genes
   📋 obs columns: 572
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Timing: 1 unique values
      - Org_celltype: 17 unique values
      - n_genes: 2414 unique values
      - doublet_scores: 115 unique values
      - predicted_doublets: 1 unique values
      - leiden: 16 unique values
      - UMAP_X: 8891 unique values
      ... and 562 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (8891, 2)
   X range: [-6.19, 11.92]
   Y range: [-3.54, 12.25]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP471
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP471/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP471/SP471.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,000 cells × 3,000 genes
   📋 obs columns: 611
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 2 unique values
      - nCount_RNA: 4721 unique values
      - nFeature_RNA: 2713 unique values
      - orig.file: 2 unique values
      - RNA_snn_res.0.5: 55 unique values
      - seurat_clusters: 55 unique values
      - dendro_order: 55 unique values
      - Org_celltype: 9 unique values
      - cell_type: 45 unique values
      - Tissue: 1 unique values
      ... and 601 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10000, 2)
   X range: [-9.68, 28.64]
   Y range: [-14.52, 26.28]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP477
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP477/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP477/SP477.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,311 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2540 unique values
      - doublet_scores: 207 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13311, 2)
   X range: [-3.15, 18.73]
   Y range: [-6.60, 22.02]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP491
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP491/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP491/SP491.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 18,912 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 6 unique values
      - n_genes: 2796 unique values
      - doublet_scores: 248 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (18912, 2)
   X range: [-9.32, 16.22]
   Y range: [-5.02, 20.94]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP492
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP492/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP492/SP492.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,992 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 10 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 3101 unique values
      - doublet_scores: 272 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (22992, 2)
   X range: [-5.11, 20.55]
   Y range: [-8.83, 18.92]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP522
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP522/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP522/SP522.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 5,894 cells × 3,000 genes
   📋 obs columns: 597
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 3 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 3 unique values
      - CellType: 3 unique values
      - Anno_Human: 3 unique values
      - Anno_Mouse: 1 unique values
      - n_genes: 1910 unique values
      - doublet_scores: 105 unique values
      ... and 587 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (5894, 2)
   X range: [-9.09, 15.01]
   Y range: [-10.53, 15.90]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP537
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP537/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP537/SP537.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,002 cells × 3,000 genes
   📋 obs columns: 618
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - orig.ident: 8 unique values
      - nCount_RNA: 6794 unique values
      - nFeature_RNA: 4130 unique values
      - orig.file: 8 unique values
      - animal: 3 unique values
      - RNA_snn_res.0.5: 59 unique values
      - seurat_clusters: 51 unique values
      - Org_celltype: 10 unique values
      - integrated_snn_res.0.5: 51 unique values
      - dendro_order: 51 unique values
      ... and 608 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10002, 2)
   X range: [-8.84, 20.92]
   Y range: [-5.75, 23.91]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP546
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP546/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP546/SP546.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 7,181 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 4 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 2 unique values
      - n_genes: 1753 unique values
      - doublet_scores: 96 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (7181, 2)
   X range: [-3.95, 18.92]
   Y range: [-10.64, 15.78]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP560
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP560/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP560/SP560.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,513 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 4 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 6 unique values
      - CellType: 4 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 1434 unique values
      - doublet_scores: 230 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13513, 2)
   X range: [-1.26, 19.38]
   Y range: [-3.55, 19.38]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP567
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP567/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP567/SP567.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 24,729 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 6 unique values
      - n_genes: 2950 unique values
      - doublet_scores: 361 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (24729, 2)
   X range: [-8.18, 14.46]
   Y range: [-5.92, 17.34]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP568
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP568/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP568/SP568.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 25,977 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 3447 unique values
      - doublet_scores: 301 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (25977, 2)
   X range: [-10.74, 14.19]
   Y range: [-9.62, 18.67]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP569
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP569/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP569/SP569.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 20,728 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 6 unique values
      - n_genes: 2775 unique values
      - doublet_scores: 268 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (20728, 2)
   X range: [-4.63, 19.84]
   Y range: [-10.59, 16.43]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP583
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP583/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP583/SP583.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,885 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 6 unique values
      - n_genes: 3158 unique values
      - doublet_scores: 245 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16885, 2)
   X range: [-9.33, 15.21]
   Y range: [-9.18, 18.18]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP587
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP587/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP587/SP587.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 11,447 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 2 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 2 unique values
      - Anno_Mouse: 2 unique values
      - n_genes: 1599 unique values
      - doublet_scores: 201 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (11447, 2)
   X range: [-5.36, 18.09]
   Y range: [-7.83, 12.27]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP598
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP598/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP598/SP598.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,891 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 5 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2625 unique values
      - doublet_scores: 207 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15891, 2)
   X range: [-5.30, 16.99]
   Y range: [-9.57, 12.31]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP709
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP709/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP709/SP709.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 30,003 cells × 3,000 genes
   📋 obs columns: 6
   🗺️  obsm keys: []

   Sample obs columns:
      - Org_celltype: 74 unique values
      - Sample: 14 unique values
      - _index: 30003 unique values
      - category: 12 unique values
      - n_genes: 4119 unique values
      - n_genes_by_counts: 1 unique values

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP799
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP799/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP799/SP799.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 16,703 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 3224 unique values
      - doublet_scores: 229 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (16703, 2)
   X range: [-5.24, 21.45]
   Y range: [-8.17, 18.96]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP815
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP815/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP815/SP815.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 12,025 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2783 unique values
      - doublet_scores: 98 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (12025, 2)
   X range: [-5.59, 20.88]
   Y range: [-4.56, 18.11]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP816
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP816/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP816/SP816.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 26,201 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 4 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 4 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 3759 unique values
      - doublet_scores: 246 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (26201, 2)
   X range: [-8.24, 14.88]
   Y range: [-7.06, 17.52]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP820
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP820/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP820/SP820.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 20,395 cells × 3,000 genes
   📋 obs columns: 11
   🗺️  obsm keys: []

   Sample obs columns:
      - Anno_Mouse: 4 unique values
      - CellType: 5 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - Org_celltype: 5 unique values
      - Region: 1 unique values
      - Tissue: 1 unique values
      - _index: 20395 unique values
      - doublet_scores: 273 unique values
      - n_genes: 1763 unique values
      ... and 1 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

❌ UMAP coordinates not found!
   Available obsm keys: []

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP824
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP824/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP824/SP824.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,900 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 1567 unique values
      - doublet_scores: 232 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15900, 2)
   X range: [-2.66, 16.32]
   Y range: [-9.53, 14.76]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP825
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP825/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP825/SP825.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 13,978 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 1975 unique values
      - doublet_scores: 218 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (13978, 2)
   X range: [-2.88, 19.65]
   Y range: [-4.26, 17.82]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP839
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP839/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP839/SP839.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 20,411 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 1725 unique values
      - doublet_scores: 269 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (20411, 2)
   X range: [-10.41, 13.14]
   Y range: [-4.75, 17.03]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP841
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP841/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP841/SP841.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 11,771 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 2785 unique values
      - doublet_scores: 204 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (11771, 2)
   X range: [-7.95, 20.38]
   Y range: [-6.80, 19.03]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP843
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP843/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP843/SP843.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 22,526 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 2263 unique values
      - doublet_scores: 359 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (22526, 2)
   X range: [-1.66, 17.45]
   Y range: [-8.56, 12.32]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP844
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP844/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP844/SP844.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 18,336 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 5 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 2 unique values
      - n_genes: 2858 unique values
      - doublet_scores: 236 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (18336, 2)
   X range: [-2.46, 16.81]
   Y range: [-8.82, 14.76]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP859
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP859/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP859/SP859.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 21,584 cells × 3,000 genes
   📋 obs columns: 578
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Human: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 3017 unique values
      - doublet_scores: 313 unique values
      ... and 568 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (21584, 2)
   X range: [-3.50, 15.94]
   Y range: [-7.06, 14.12]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP864
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP864/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP864/SP864.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 14,562 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 3969 unique values
      - doublet_scores: 221 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (14562, 2)
   X range: [-4.71, 21.57]
   Y range: [-10.03, 17.78]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP881
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP881/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP881/SP881.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 20,907 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 7 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 2298 unique values
      - doublet_scores: 260 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (20907, 2)
   X range: [-7.88, 15.27]
   Y range: [-5.77, 20.36]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP884
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP884/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP884/SP884.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 15,349 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2540 unique values
      - doublet_scores: 238 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (15349, 2)
   X range: [-4.61, 17.77]
   Y range: [-9.49, 14.31]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP886
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP886/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP886/SP886.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 10,002 cells × 3,000 genes
   📋 obs columns: 505
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - SampleID: 2 unique values
      - Age: 2 unique values
      - Org_celltype: 25 unique values
      - Tissue: 1 unique values
      - n_genes: 3434 unique values
      - doublet_scores: 229 unique values
      - predicted_doublets: 1 unique values
      - leiden: 21 unique values
      - UMAP_X: 10002 unique values
      - UMAP_Y: 9999 unique values
      ... and 495 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (10002, 2)
   X range: [-6.03, 17.35]
   Y range: [-4.39, 17.96]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP887
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP887/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP887/SP887.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 30,962 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - Anno_Mouse: 5 unique values
      - n_genes: 2752 unique values
      - doublet_scores: 310 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (30962, 2)
   X range: [-8.01, 15.32]
   Y range: [-4.31, 17.68]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP894
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP894/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP894/SP894.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 9,894 cells × 3,000 genes
   📋 obs columns: 22
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 5 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 5 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 2 unique values
      - n_genes: 2010 unique values
      - doublet_scores: 155 unique values
      - predicted_doublets: 1 unique values
      ... and 12 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (9894, 2)
   X range: [-3.76, 18.70]
   Y range: [-5.33, 24.50]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP913
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP913/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP913/SP913.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 11,615 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 8 unique values
      - CellType: 6 unique values
      - n_genes: 3181 unique values
      - doublet_scores: 189 unique values
      - predicted_doublets: 1 unique values
      - leiden: 32 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (11615, 2)
   X range: [-8.83, 17.29]
   Y range: [-11.75, 14.53]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP914
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP914/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP914/SP914.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 21,434 cells × 3,000 genes
   📋 obs columns: 21
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 6 unique values
      - Tissue: 1 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 9 unique values
      - CellType: 6 unique values
      - n_genes: 3935 unique values
      - doublet_scores: 271 unique values
      - predicted_doublets: 1 unique values
      - leiden: 39 unique values
      ... and 11 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (21434, 2)
   X range: [-5.06, 21.73]
   Y range: [-7.60, 19.79]

🏷️  Cell type column: "laca_curated_celltype_v3"

══════════════════════════════════════════════════════════════════════
  🧬 Single Cell Atlas Data Generator (gzip compressed)
══════════════════════════════════════════════════════════════════════

🔖 SP_ID: SP920
📁 Output directory: /mnt/alamo01/projects/test_20241129/cds_test/SP920/

======================================================================
📂 Reading h5ad file: /mnt/alamo01/projects/test_20241129/LCA/SP920/SP920.h5ad
======================================================================

   ✅ Loaded successfully!
   📊 Dimensions: 45,383 cells × 3,000 genes
   📋 obs columns: 607
   🗺️  obsm keys: ['X_pca', 'X_umap']

   Sample obs columns:
      - Org_celltype: 34 unique values
      - Tissue: 3 unique values
      - Region: 1 unique values
      - DevoStage: 1 unique values
      - Old_celltype: 5 unique values
      - CellType: 5 unique values
      - Anno_Mouse: 4 unique values
      - n_genes: 5290 unique values
      - doublet_scores: 1101 unique values
      - predicted_doublets: 1 unique values
      ... and 597 more columns

📋 Loading cellinfo mapping from /mnt/alamo01/projects/test_20241129/cds_test/table/cellinfo.csv...
   Loaded 152 cell type definitions
   Columns: ['CellType_Standard', 'Abbreviation', 'Major_CellType', 'Major_CellTypeID', 'ctID', 'Mapping', 'TissueName', 'TissueID', 'SP_ID', 'SP_Count', 'CSinclude', 'ColorCode', 'CTintro', 'Homepage']
   Built 1285 name mappings
   Unique standard types: 152

======================================================================
🗺️  Generating UMAP data files
======================================================================

📍 UMAP coordinates: (45383, 2)
   X range: [-10.24, 13.36]
   Y range: [-9.67, 17.47]

🏷️  Cell type column: "laca_curated_celltype_v3"
==========================================
Job finished at: Sun Feb 15 04:48:23 AM CST 2026
==========================================
