══════════════════════════════════════════════════════════════════════
  🧬 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"

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  🧬 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

