Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/1ba5b4d7d8bfe798/CROSSWALK.json

@@ -0,0 +1,710 @@
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+      "position": 32453,
+      "seurat_name": "SLC5A3.1",
+      "tenx_symbol": "SLC5A3",
+      "ensembl_id": "ENSG00000198743"
+    },
+    {
+      "position": 32714,
+      "seurat_name": "FRG2C.1",
+      "tenx_symbol": "FRG2C",
+      "ensembl_id": "ENSG00000220903"
+    },
+    {
+      "position": 32718,
+      "seurat_name": "ZNF84.1",
+      "tenx_symbol": "ZNF84",
+      "ensembl_id": "ENSG00000218497"
+    },
+    {
+      "position": 32719,
+      "seurat_name": "ZNF26.1",
+      "tenx_symbol": "ZNF26",
+      "ensembl_id": "ENSG00000236575"
+    },
+    {
+      "position": 32728,
+      "seurat_name": "KIR3DL2.1",
+      "tenx_symbol": "KIR3DL2",
+      "ensembl_id": "ENSG00000217792"
+    },
+    {
+      "position": 32731,
+      "seurat_name": "PNRC2.1",
+      "tenx_symbol": "PNRC2",
+      "ensembl_id": "ENSG00000215700"
+    },
+    {
+      "position": 32732,
+      "seurat_name": "SRSF10.1",
+      "tenx_symbol": "SRSF10",
+      "ensembl_id": "ENSG00000215699"
+    }
+  ],
+  "file": {
+    "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/liu2021_v1_20261002/reference_crosswalk/cellranger_hg19-1.2.0_features__from_GSE206283_GSM6249265.tsv.gz",
+    "sha256": "d0bdfea9e111c174bb2dd81fd63a8bbaf93829c0d1bef396aaf2f3b6b5774a58",
+    "bytes": 310002
+  },
+  "copied_from": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/giroux2022_v1_20260928/extracted/GSE206283/GSM6249265/scRNA_59-0_filtered_feature_bc_matrix/features.tsv.gz",
+  "origin": {
+    "geo_archive": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE206283/raw/GSE206283_RAW.tar",
+    "url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE206nnn/GSE206283/suppl/GSE206283_RAW.tar",
+    "sha256": "17599bb1fca707204353c69b07c1f90a7784aa9664a419dbe99416df789b0729",
+    "matches_receipt": true,
+    "note": "Giroux 2022 GEO per-GSM Cell Ranger 3.1.0 hg19 matrices; all 41 features.tsv copies are byte-identical (Giroux FINDINGS sc_chemistry)"
+  },
+  "paper_statement": "GEO GSE161918 data processing: 'Genome_build: hg19 (cellranger version 1.2.0)'; mapping CellRanger 3.1.0",
+  "created_utc": "2026-10-02T12:15:50.923337+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/300949d2c1441865/assemble.log

@@ -0,0 +1,259 @@
+2026-10-02T21:20:00+09:00 launch assemble MemAvailable 103 GiB
+B1_AA220014_HC AA220014_HC: 419 cells, nnz 184408
+B1_AA220534_HC AA220534_HC: 353 cells, nnz 136231
+B1_AA220907_HC AA220907_HC: 381 cells, nnz 144642
+B1_HGR0000071_T0 HGR0000071_T0: 341 cells, nnz 121677
+B1_HGR0000074_T0 HGR0000074_T0: 335 cells, nnz 114622
+B1_HGR0000078_T0 HGR0000078_T0: 184 cells, nnz 60916
+B1_HGR0000078_T1 HGR0000078_T1: 199 cells, nnz 69885
+B1_HGR0000079_T0 HGR0000079_T0: 114 cells, nnz 39413
+B1_HGR0000079_T1 HGR0000079_T1: 141 cells, nnz 54212
+B1_HGR0000083_T0 HGR0000083_T0: 158 cells, nnz 54342
+B1_HGR0000083_T1 HGR0000083_T1: 299 cells, nnz 132892
+B1_HGR0000089_T1 HGR0000089_T1: 358 cells, nnz 130186
+B1_HGR0000091_T0 HGR0000091_T0: 362 cells, nnz 136701
+B1_HGR0000093_T0 HGR0000093_T0: 451 cells, nnz 167162
+B1_HGR0000093_T1 HGR0000093_T1: 152 cells, nnz 54670
+B1_HGR0000098_T0 HGR0000098_T0: 390 cells, nnz 140758
+B1_HGR0000110_T0 HGR0000110_T0: 128 cells, nnz 32211
+B1_HGR0000136_T0 HGR0000136_T0: 317 cells, nnz 122154
+B1_HGR0000137_T0 HGR0000137_T0: 314 cells, nnz 114036
+B1_HGR0000141_T0 HGR0000141_T0: 240 cells, nnz 87295
+B1_HGR0000143_T0 HGR0000143_T0: 280 cells, nnz 96234
+B1_IM000040_HC IM000040_HC: 373 cells, nnz 154950
+B2_HGR0000042_T0 HGR0000042_T0: 2213 cells, nnz 1030336
+B2_HGR0000042_T1 HGR0000042_T1: 4514 cells, nnz 1846053
+B2_HGR0000069_T0 HGR0000069_T0: 4419 cells, nnz 1745599
+B2_HGR0000069_T1 HGR0000069_T1: 4418 cells, nnz 1895474
+B2_HGR0000069_T2 HGR0000069_T2: 2351 cells, nnz 1092589
+B2_HGR0000092_T0 HGR0000092_T0: 5316 cells, nnz 2255309
+B2_HGR0000092_T1 HGR0000092_T1: 2917 cells, nnz 1423077
+B2_HGR0000094_T0 HGR0000094_T0: 3045 cells, nnz 1236078
+B2_HGR0000094_T1 HGR0000094_T1: 908 cells, nnz 401278
+B2_HGR0000115_T1 HGR0000115_T1: 5186 cells, nnz 2128578
+B2_HGR0000124_T0 HGR0000124_T0: 8731 cells, nnz 3662724
+B2_HGR0000124_T1 HGR0000124_T1: 2515 cells, nnz 1224474
+B2_HGR0000144_T0 HGR0000144_T0: 2243 cells, nnz 1027210
+B2_HGR0000144_T2 HGR0000144_T2: 6257 cells, nnz 2477454
+B2_HGR0000391_T0 HGR0000391_T0: 6728 cells, nnz 2871381
+B2_HGR0000395_T0 HGR0000395_T0: 2786 cells, nnz 1298084
+B2_HGR0000418_T1 HGR0000418_T1: 6151 cells, nnz 2557702
+B2_SHD2_HC SHD2_HC: 3484 cells, nnz 1699075
+B2_SHD4_HC SHD4_HC: 7126 cells, nnz 3300335
+B2_SHD7_HC SHD7_HC: 6375 cells, nnz 2932412
+B3_HGR0000051_T0 HGR0000051_T0: 2947 cells, nnz 1252010
+B3_HGR0000051_T1 HGR0000051_T1: 4888 cells, nnz 1990803
+B3_HGR0000051_T2 HGR0000051_T2: 2109 cells, nnz 966725
+B3_HGR0000051_T3 HGR0000051_T3: 5007 cells, nnz 1969378
+B3_HGR0000101_T0 HGR0000101_T0: 920 cells, nnz 402819
+B3_HGR0000101_T1 HGR0000101_T1: 4781 cells, nnz 1988998
+B3_HGR0000101_T3 HGR0000101_T3: 3855 cells, nnz 1624688
+B3_HGR0000102_T0 HGR0000102_T0: 4533 cells, nnz 2019940
+B3_HGR0000102_T1 HGR0000102_T1: 5393 cells, nnz 2336004
+B3_HGR0000134_T0 HGR0000134_T0: 5941 cells, nnz 2685662
+B3_HGR0000134_T1 HGR0000134_T1: 2705 cells, nnz 1247002
+B3_HGR0000135_T0 HGR0000135_T0: 5972 cells, nnz 2449337
+B3_HGR0000135_T1 HGR0000135_T1: 4829 cells, nnz 2087980
+B3_HGR0000142_T0 HGR0000142_T0: 2766 cells, nnz 1194281
+B3_HGR0000392_T0 HGR0000392_T0: 5261 cells, nnz 2253922
+B3_HGR0000392_T3 HGR0000392_T3: 1413 cells, nnz 609357
+B3_HGR0000429_T1 HGR0000429_T1: 7249 cells, nnz 3083508
+B3_HGR0000429_T2 HGR0000429_T2: 4895 cells, nnz 2123793
+B3_HGR0000430_T1 HGR0000430_T1: 1875 cells, nnz 844110
+B3_SHD1_HC SHD1_HC: 6174 cells, nnz 2695329
+B3_SHD3_HC SHD3_HC: 5175 cells, nnz 2387702
+B3_SHD5_HC SHD5_HC: 6397 cells, nnz 2950216
+B3_SHD6_HC SHD6_HC: 2487 cells, nnz 1157311
+{
+ "rows": 65,
+ "cells": {
+  "n_cells": 191544,
+  "nnz": 82775694,
+  "per_row_min": 114,
+  "per_row_median": 2705.0,
+  "per_row_max": 8731,
+  "median_umi_per_cell_canonical": 4384.0,
+  "median_umi_per_cell_source": 4613.0
+ },
+ "checks": {
+  "gene_positions_sha256_ok": true,
+  "panel_gene_ids_match_selected_genes_csv": true,
+  "panel_gene_ids_match_giroux2022_cells_panel6k": true,
+  "bulk_integer_nonnegative_inside_mask": true,
+  "bulk_raw_nan_exactly_outside_bulk_valid": true,
+  "pseudo_raw_sum_equals_sum_of_retained_cells_full_axis": true,
+  "cells_panel_sums_equal_pseudo_raw_sum_positions_exactly": true,
+  "cells_per_row_equal_qc_cell_counts": true,
+  "no_sc_mass_outside_sc_valid": true,
+  "one_sample_id_per_library": true,
+  "sc_cells_are_unsorted_hto_singlet_demuxlet_singlet": true,
+  "sex_concordant_pairs": "58/65",
+  "expression_best_match_is_own_pair": "25/65",
+  "expression_best_match_is_own_pair_centred": "40/65",
+  "expression_reverse_best_match_is_own_pair": "17/65",
+  "expression_residualised_k5_own_subject_top1_bulk_to_sc": "62/65",
+  "expression_residualised_k3_own_subject_top1_bulk_to_sc": "61/65",
+  "expression_residualised_k10_own_subject_top1_bulk_to_sc": "60/65",
+  "expression_residualised_k5_own_subject_top1_sc_to_bulk": "63/65",
+  "expression_residualised_k3_own_subject_top1_sc_to_bulk": "64/65",
+  "expression_residualised_k10_own_subject_top1_sc_to_bulk": "62/65",
+  "expression_residualised_k5_own_library_top1_bulk_to_sc": "61/65",
+  "expression_residualised_k3_own_library_top1_bulk_to_sc": "59/65",
+  "expression_residualised_k10_own_library_top1_bulk_to_sc": "60/65",
+  "expression_residualised_k5_own_timepoint_best_within_subject_bulk_to_sc_multi_timepoint_rows": "37/38",
+  "expression_residualised_k5_own_timepoint_best_within_subject_sc_to_bulk_multi_timepoint_rows": "37/38",
+  "expression_centred_own_timepoint_best_within_subject_bulk_to_sc_multi_timepoint_rows": "30/38",
+  "expression_centred_own_timepoint_best_within_subject_sc_to_bulk_multi_timepoint_rows": "34/38",
+  "isg_peak_timepoint_same_in_both_assays_multi_timepoint_subjects": "16/17",
+  "identity_check_pass": "57/65",
+  "identity_check_fail": [
+   "AA220907_HC",
+   "HGR0000078_T0",
+   "HGR0000078_T1",
+   "HGR0000079_T0",
+   "HGR0000079_T1",
+   "HGR0000110_T0",
+   "HGR0000144_T0",
+   "HGR0000144_T2"
+  ],
+  "identity_check_borderline": [],
+  "rows_below_200_cells": [
+   "HGR0000078_T0",
+   "HGR0000078_T1",
+   "HGR0000079_T0",
+   "HGR0000079_T1",
+   "HGR0000083_T0",
+   "HGR0000093_T1",
+   "HGR0000110_T0"
+  ],
+  "usable_rows_identity_pass_and_ge_200_cells": 55
+ }
+}
+2026-10-02T21:21:52+09:00 launch assemble MemAvailable 103 GiB
+B1_AA220014_HC AA220014_HC: 419 cells, nnz 184408
+B1_AA220534_HC AA220534_HC: 353 cells, nnz 136231
+B1_AA220907_HC AA220907_HC: 381 cells, nnz 144642
+B1_HGR0000071_T0 HGR0000071_T0: 341 cells, nnz 121677
+B1_HGR0000074_T0 HGR0000074_T0: 335 cells, nnz 114622
+B1_HGR0000078_T0 HGR0000078_T0: 184 cells, nnz 60916
+B1_HGR0000078_T1 HGR0000078_T1: 199 cells, nnz 69885
+B1_HGR0000079_T0 HGR0000079_T0: 114 cells, nnz 39413
+B1_HGR0000079_T1 HGR0000079_T1: 141 cells, nnz 54212
+B1_HGR0000083_T0 HGR0000083_T0: 158 cells, nnz 54342
+B1_HGR0000083_T1 HGR0000083_T1: 299 cells, nnz 132892
+B1_HGR0000089_T1 HGR0000089_T1: 358 cells, nnz 130186
+B1_HGR0000091_T0 HGR0000091_T0: 362 cells, nnz 136701
+B1_HGR0000093_T0 HGR0000093_T0: 451 cells, nnz 167162
+B1_HGR0000093_T1 HGR0000093_T1: 152 cells, nnz 54670
+B1_HGR0000098_T0 HGR0000098_T0: 390 cells, nnz 140758
+B1_HGR0000110_T0 HGR0000110_T0: 128 cells, nnz 32211
+B1_HGR0000136_T0 HGR0000136_T0: 317 cells, nnz 122154
+B1_HGR0000137_T0 HGR0000137_T0: 314 cells, nnz 114036
+B1_HGR0000141_T0 HGR0000141_T0: 240 cells, nnz 87295
+B1_HGR0000143_T0 HGR0000143_T0: 280 cells, nnz 96234
+B1_IM000040_HC IM000040_HC: 373 cells, nnz 154950
+B2_HGR0000042_T0 HGR0000042_T0: 2213 cells, nnz 1030336
+B2_HGR0000042_T1 HGR0000042_T1: 4514 cells, nnz 1846053
+B2_HGR0000069_T0 HGR0000069_T0: 4419 cells, nnz 1745599
+B2_HGR0000069_T1 HGR0000069_T1: 4418 cells, nnz 1895474
+B2_HGR0000069_T2 HGR0000069_T2: 2351 cells, nnz 1092589
+B2_HGR0000092_T0 HGR0000092_T0: 5316 cells, nnz 2255309
+B2_HGR0000092_T1 HGR0000092_T1: 2917 cells, nnz 1423077
+B2_HGR0000094_T0 HGR0000094_T0: 3045 cells, nnz 1236078
+B2_HGR0000094_T1 HGR0000094_T1: 908 cells, nnz 401278
+B2_HGR0000115_T1 HGR0000115_T1: 5186 cells, nnz 2128578
+B2_HGR0000124_T0 HGR0000124_T0: 8731 cells, nnz 3662724
+B2_HGR0000124_T1 HGR0000124_T1: 2515 cells, nnz 1224474
+B2_HGR0000144_T0 HGR0000144_T0: 2243 cells, nnz 1027210
+B2_HGR0000144_T2 HGR0000144_T2: 6257 cells, nnz 2477454
+B2_HGR0000391_T0 HGR0000391_T0: 6728 cells, nnz 2871381
+B2_HGR0000395_T0 HGR0000395_T0: 2786 cells, nnz 1298084
+B2_HGR0000418_T1 HGR0000418_T1: 6151 cells, nnz 2557702
+B2_SHD2_HC SHD2_HC: 3484 cells, nnz 1699075
+B2_SHD4_HC SHD4_HC: 7126 cells, nnz 3300335
+B2_SHD7_HC SHD7_HC: 6375 cells, nnz 2932412
+B3_HGR0000051_T0 HGR0000051_T0: 2947 cells, nnz 1252010
+B3_HGR0000051_T1 HGR0000051_T1: 4888 cells, nnz 1990803
+B3_HGR0000051_T2 HGR0000051_T2: 2109 cells, nnz 966725
+B3_HGR0000051_T3 HGR0000051_T3: 5007 cells, nnz 1969378
+B3_HGR0000101_T0 HGR0000101_T0: 920 cells, nnz 402819
+B3_HGR0000101_T1 HGR0000101_T1: 4781 cells, nnz 1988998
+B3_HGR0000101_T3 HGR0000101_T3: 3855 cells, nnz 1624688
+B3_HGR0000102_T0 HGR0000102_T0: 4533 cells, nnz 2019940
+B3_HGR0000102_T1 HGR0000102_T1: 5393 cells, nnz 2336004
+B3_HGR0000134_T0 HGR0000134_T0: 5941 cells, nnz 2685662
+B3_HGR0000134_T1 HGR0000134_T1: 2705 cells, nnz 1247002
+B3_HGR0000135_T0 HGR0000135_T0: 5972 cells, nnz 2449337
+B3_HGR0000135_T1 HGR0000135_T1: 4829 cells, nnz 2087980
+B3_HGR0000142_T0 HGR0000142_T0: 2766 cells, nnz 1194281
+B3_HGR0000392_T0 HGR0000392_T0: 5261 cells, nnz 2253922
+B3_HGR0000392_T3 HGR0000392_T3: 1413 cells, nnz 609357
+B3_HGR0000429_T1 HGR0000429_T1: 7249 cells, nnz 3083508
+B3_HGR0000429_T2 HGR0000429_T2: 4895 cells, nnz 2123793
+B3_HGR0000430_T1 HGR0000430_T1: 1875 cells, nnz 844110
+B3_SHD1_HC SHD1_HC: 6174 cells, nnz 2695329
+B3_SHD3_HC SHD3_HC: 5175 cells, nnz 2387702
+B3_SHD5_HC SHD5_HC: 6397 cells, nnz 2950216
+B3_SHD6_HC SHD6_HC: 2487 cells, nnz 1157311
+{
+ "rows": 65,
+ "cells": {
+  "n_cells": 191544,
+  "nnz": 82775694,
+  "per_row_min": 114,
+  "per_row_median": 2705.0,
+  "per_row_max": 8731,
+  "median_umi_per_cell_canonical": 4384.0,
+  "median_umi_per_cell_source": 4613.0
+ },
+ "checks": {
+  "gene_positions_sha256_ok": true,
+  "panel_gene_ids_match_selected_genes_csv": true,
+  "panel_gene_ids_match_giroux2022_cells_panel6k": true,
+  "bulk_integer_nonnegative_inside_mask": true,
+  "bulk_raw_nan_exactly_outside_bulk_valid": true,
+  "pseudo_raw_sum_equals_sum_of_retained_cells_full_axis": true,
+  "cells_panel_sums_equal_pseudo_raw_sum_positions_exactly": true,
+  "cells_per_row_equal_qc_cell_counts": true,
+  "no_sc_mass_outside_sc_valid": true,
+  "one_sample_id_per_library": true,
+  "sc_cells_are_unsorted_hto_singlet_demuxlet_singlet": true,
+  "sex_concordant_pairs": "63/65",
+  "expression_best_match_is_own_pair": "25/65",
+  "expression_best_match_is_own_pair_centred": "40/65",
+  "expression_reverse_best_match_is_own_pair": "17/65",
+  "expression_residualised_k5_own_subject_top1_bulk_to_sc": "62/65",
+  "expression_residualised_k3_own_subject_top1_bulk_to_sc": "61/65",
+  "expression_residualised_k10_own_subject_top1_bulk_to_sc": "60/65",
+  "expression_residualised_k5_own_subject_top1_sc_to_bulk": "63/65",
+  "expression_residualised_k3_own_subject_top1_sc_to_bulk": "64/65",
+  "expression_residualised_k10_own_subject_top1_sc_to_bulk": "62/65",
+  "expression_residualised_k5_own_library_top1_bulk_to_sc": "61/65",
+  "expression_residualised_k3_own_library_top1_bulk_to_sc": "59/65",
+  "expression_residualised_k10_own_library_top1_bulk_to_sc": "60/65",
+  "expression_residualised_k5_own_timepoint_best_within_subject_bulk_to_sc_multi_timepoint_rows": "37/38",
+  "expression_residualised_k5_own_timepoint_best_within_subject_sc_to_bulk_multi_timepoint_rows": "37/38",
+  "expression_centred_own_timepoint_best_within_subject_bulk_to_sc_multi_timepoint_rows": "30/38",
+  "expression_centred_own_timepoint_best_within_subject_sc_to_bulk_multi_timepoint_rows": "34/38",
+  "isg_peak_timepoint_same_in_both_assays_multi_timepoint_subjects": "16/17",
+  "identity_check_pass": "61/65",
+  "identity_check_fail": [
+   "HGR0000079_T0",
+   "HGR0000079_T1",
+   "HGR0000110_T0"
+  ],
+  "identity_check_borderline": [
+   "HGR0000078_T0"
+  ],
+  "rows_below_200_cells": [
+   "HGR0000078_T0",
+   "HGR0000078_T1",
+   "HGR0000079_T0",
+   "HGR0000079_T1",
+   "HGR0000083_T0",
+   "HGR0000093_T1",
+   "HGR0000110_T0"
+  ],
+  "usable_rows_identity_pass_and_ge_200_cells": 58
+ }
+}

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/515ed8928d81f3c1/sc_without_bulk.csv

@@ -0,0 +1,6 @@
+sc_sample,Batch,Donor,Subject,Timepoint,Class,Age,Gender,Ward,Status,symptom_type,hospital_days,day_from_symptom_onset_to_hospitalization,number_of_days_hospitalized,computed_ethnicity,ever_admitted_to_icu,severity,days_of_symptoms_onset,condition,outcome,DDimer,CRP,material_type,sample_bsi_id,sample_alt_id,sample_label,batch,days_since_hospitalized,days_since_onset,severity.outcome,PC1,PC1_cat,cond_group,onset_group,intubation_vent,PC1_onset_group,sample_name,Sorted,BatchSort,n_cells_object,n_sorted_dropped,n_unsorted,n_unsorted_hto_singlet,n_unsorted_hto_doublet,n_unsorted_hto_negative,n_unsorted_not_demuxlet_singlet,n_selected,hashtags,kind,reason
+B1_CHI014_HC,B1,CHI014,CHI014,HC,HC,,na,Healthy_control,na,HC,0,,,,,,0,,,,,,,,,,,,,,,HC,,,NA_NA,CHI014_HC,N,B1UnSort,2744,2164,580,545,35,0,0,545,HTO1|HTO2,technical_control,technical control (CHI014 / HD buffy-coat test donor); excluded by task rule
+B2_CHI014_HC,B2,CHI014,CHI014,HC,HC,,na,Healthy_control,na,HC,0,,,,,,0,,,,,,,,,,,,,,,HC,,,NA_NA,CHI014_HC,N,B2UnSort,9222,2423,6799,5815,3,981,0,5815,HTO1|HTO2|HTO3,technical_control,technical control (CHI014 / HD buffy-coat test donor); excluded by task rule
+B2_HDML_PBMC_HC,B2,HDML,HDML_PBMC,HC,HC,45,Male,Healthy_control,na,HC,0,,,,,,0,,,,,,,,,,,,,,,HC,,,NA_NA,HDML_PBMC_HC,N,B2UnSort,9618,2268,7350,7191,3,156,0,7191,HTO1,technical_control,technical control (CHI014 / HD buffy-coat test donor); excluded by task rule
+B2_HDVO_PBMC_HC,B2,HDVO,HDVO_PBMC,HC,HC,30,Male,Healthy_control,na,HC,0,,,,,,0,,,,,,,,,,,,,,,HC,,,NA_NA,HDVO_PBMC_HC,N,B2UnSort,10568,3884,6684,6664,6,14,0,6664,HTO2,technical_control,technical control (CHI014 / HD buffy-coat test donor); excluded by task rule
+B3_CHI014_HC,B3,CHI014,CHI014,HC,HC,,na,Healthy_control,na,HC,0,,,,,,0,,,,,,,,,,,,,,,HC,,,NA_NA,CHI014_HC,N,B3UnSort,14018,4837,9181,7737,87,1357,0,7737,HTO1|HTO2|HTO3|HTO5,technical_control,technical control (CHI014 / HD buffy-coat test donor); excluded by task rule

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/7fceeaebcb0ba6f1/PAIRING_SUMMARY.json

@@ -0,0 +1,186 @@
+{
+  "bulk_gsms": 73,
+  "bulk_columns": 73,
+  "bulk_columns_by_table": {
+    "B2_B3_bulkRNAseq_countmtx.csv": 50,
+    "B1_bulkRNAseq_countmtx.csv": 23
+  },
+  "bulk_columns_by_kind": {
+    "COVID": 54,
+    "HC": 11,
+    "technical_control": 7,
+    "author_excluded": 1
+  },
+  "bulk_column_corrections": [
+    {
+      "bulk_column": "PHGR0000074_T0",
+      "column_key": "HGR0000074_T0",
+      "bulk_gsm": "GSM4929238",
+      "bulk_title": "Batch 1 bulk RNAseq HGR0000074"
+    }
+  ],
+  "bulk_timepoint_conflicts": [
+    {
+      "bulk_column": "HGR0000089_T1",
+      "bulk_gsm": "GSM4929245",
+      "bulk_title": "Batch 1 bulk RNAseq HGR0000089",
+      "timepoint_conflict": "column name T1 vs GEO characteristic 'Timepoint 0'"
+    }
+  ],
+  "bulk_material": "GEO source 'Peripheral Blood Mononuclear Cells', characteristic 'Unsorted' for all 73 bulk GSMs",
+  "sc_cells_object": 411902,
+  "sc_cells_unsorted": 260456,
+  "sc_cells_selected": 224919,
+  "sc_cells_by_batchsort_hto": {
+    "Doublet": {
+      "B1Sort": 10732,
+      "B1UnSort": 358,
+      "B2Sort": 596,
+      "B2UnSort": 98,
+      "B3Sort": 0,
+      "B3UnSort": 1426
+    },
+    "Negative": {
+      "B1Sort": 0,
+      "B1UnSort": 0,
+      "B2Sort": 0,
+      "B2UnSort": 15723,
+      "B3Sort": 148,
+      "B3UnSort": 17932
+    },
+    "Singlet": {
+      "B1Sort": 23605,
+      "B1UnSort": 6982,
+      "B2Sort": 49582,
+      "B2UnSort": 109828,
+      "B3Sort": 66783,
+      "B3UnSort": 108109
+    }
+  },
+  "sc_droplet_type": {
+    "SNG": 411902
+  },
+  "sc_samples_unsorted": 70,
+  "sc_samples_by_kind": {
+    "COVID": 54,
+    "HC": 11,
+    "technical_control": 5
+  },
+  "hto_metadata_cross_check": {
+    "cells": 411902,
+    "cells_key_found": 411902,
+    "timepoint_agrees": 411902,
+    "timepoint_agrees_selected": 224919,
+    "batch1_sorted_agrees": 41677,
+    "batch1_cells": 41677,
+    "selected_cells": 224919,
+    "selected_key_not_found": {},
+    "selected_timepoint_disagrees": {},
+    "key": "Batch + '|' + Donor + '_' + autoHashcalls (the hashtag that defines the author Sample)"
+  },
+  "pairs_total": 65,
+  "pairs_subjects": 44,
+  "pairs_by_group": {
+    "COVID": 54,
+    "HC": 11
+  },
+  "pairs_by_timepoint": {
+    "T0": 28,
+    "T1": 19,
+    "HC": 11,
+    "T2": 4,
+    "T3": 3
+  },
+  "pairs_by_batch": {
+    "B3": 23,
+    "B1": 22,
+    "B2": 20
+  },
+  "pairs_by_id_match": {
+    "exact_subject_timepoint": 63,
+    "subject_timepoint; bulk column name corrected": 1,
+    "subject_timepoint; GEO bulk timepoint characteristic differs": 1
+  },
+  "subjects_by_group": {
+    "COVID": 33,
+    "HC": 11
+  },
+  "sc_without_bulk": [
+    {
+      "sc_sample": "B1_CHI014_HC",
+      "kind": "technical_control",
+      "reason": "technical control (CHI014 / HD buffy-coat test donor); excluded by task rule"
+    },
+    {
+      "sc_sample": "B2_CHI014_HC",
+      "kind": "technical_control",
+      "reason": "technical control (CHI014 / HD buffy-coat test donor); excluded by task rule"
+    },
+    {
+      "sc_sample": "B2_HDML_PBMC_HC",
+      "kind": "technical_control",
+      "reason": "technical control (CHI014 / HD buffy-coat test donor); excluded by task rule"
+    },
+    {
+      "sc_sample": "B2_HDVO_PBMC_HC",
+      "kind": "technical_control",
+      "reason": "technical control (CHI014 / HD buffy-coat test donor); excluded by task rule"
+    },
+    {
+      "sc_sample": "B3_CHI014_HC",
+      "kind": "technical_control",
+      "reason": "technical control (CHI014 / HD buffy-coat test donor); excluded by task rule"
+    }
+  ],
+  "bulk_without_sc": [
+    {
+      "bulk_column": "CHI-014",
+      "bulk_gsm": "GSM4929236",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "CHI014_B2",
+      "bulk_gsm": "GSM4929256",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "CHI014_B3",
+      "bulk_gsm": "GSM4929282",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "HD_ML_bc",
+      "bulk_gsm": "GSM4929257",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "HD_ML_PBMC",
+      "bulk_gsm": "GSM4929258",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "HD_VO_bc",
+      "bulk_gsm": "GSM4929259",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "HD_VO_PBMC",
+      "bulk_gsm": "GSM4929260",
+      "kind": "technical_control",
+      "unpaired_reason": "technical control column (CHI014 / HD buffy-coat test); excluded by task rule"
+    },
+    {
+      "bulk_column": "SHD8",
+      "bulk_gsm": "GSM4929281",
+      "kind": "author_excluded",
+      "unpaired_reason": "GEO: 'Healthy Control (excluded due to abnormal lymphoma-like B cells found upon analysis)'; the author Seurat object holds 0 cells of this subject"
+    }
+  ],
+  "rule": "A pair is one author bulk count-table column and one author sc sample (unsorted fraction) with the same subject and the same timepoint label (T0-T3, or HC). Bulk column <-> GEO GSM by the GEO title name within the same count table (1:1, all 73). Column subject/timepoint from the column name (one typo corrected: PHGR0000074_T0); the sc subject/timepoint are the author metadata Subject and Timepoint (hashtag-defined; cross-checked against the GEO HTO/timepoint table). Technical controls (CHI014, HD_ML/HD_VO) are not paired. No expression, age-sex or order matching creates a pair."
+}