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  1. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/1cc0065a3e8d2934/htosens.log +34 -0
  2. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/8707931c36a42f54/prepare.log +53 -0
  3. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/919f79a25e62b30c/rds.log +12 -0
  4. paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/e2ebdf8a70b58cfd/pairing.log +2 -0
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/1cc0065a3e8d2934/htosens.log ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ 2026-10-02T21:37:52+09:00 launch htosens MemAvailable 109 GiB
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+ {
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+ "genes": 32362,
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+ "rows_with_>=50_negative_cells": 20,
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+ "median_negative_fraction_those_rows": 0.403779248910689,
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+ "r_own_singlet_median": 0.9182934727603804,
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+ "r_own_negative_median": 0.9005794797648514,
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+ "r_own_singlet_plus_negative_median": 0.9178280617774,
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+ "rows_where_adding_negatives_raises_r_own": 7,
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+ "negatives_own_timepoint_beats_best_other_timepoint": "10/14",
11
+ "singlets_own_timepoint_beats_best_other_timepoint": "12/14",
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+ "note": "r over hg19 symbols shared by the 10x table (unique) and the bulk table; informational only - the dataset keeps the task rule (HTO singlets only)"
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+ }
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+ sample_id sc_sample batch hashtag n_singlet_pass n_negative_pass subject_other_timepoints r_own_singlet r_own_singlet_plus_negative r_best_other_timepoint_singlet r_best_other_timepoint_singlet_plus_negative r_own_negative r_best_other_timepoint_negative negative_fraction
15
+ 22 HGR0000042_T0 B2_HGR0000042_T0 B2 HTO3 2213 1066 1 0.9205 0.9207 0.9200 0.9199 0.8994 0.8987 0.3251
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+ 25 HGR0000069_T1 B2_HGR0000069_T1 B2 HTO1 4418 750 2 0.9176 0.9169 0.9125 0.9134 0.8758 0.8976 0.1451
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+ 26 HGR0000069_T2 B2_HGR0000069_T2 B2 HTO3 2351 1779 2 0.9182 0.9173 0.9118 0.9130 0.9013 0.9024 0.4308
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+ 27 HGR0000092_T0 B2_HGR0000092_T0 B2 HTO1 5316 188 1 0.9165 0.9163 0.9126 0.9123 0.8726 0.8626 0.0342
19
+ 28 HGR0000092_T1 B2_HGR0000092_T1 B2 HTO3 2917 1402 1 0.9188 0.9216 0.9027 0.9085 0.9064 0.9050 0.3246
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+ 30 HGR0000094_T1 B2_HGR0000094_T1 B2 HTO3 908 839 1 0.9127 0.9165 0.9019 0.9092 0.9007 0.9021 0.4803
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+ 32 HGR0000124_T0 B2_HGR0000124_T0 B2 HTO2 8731 53 1 0.9184 0.9184 0.9212 0.9212 0.8298 0.8369 0.0060
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+ 33 HGR0000124_T1 B2_HGR0000124_T1 B2 HTO3 2515 1299 1 0.9233 0.9224 0.9210 0.9181 0.8974 0.8861 0.3406
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+ 34 HGR0000144_T0 B2_HGR0000144_T0 B2 HTO3 2243 1967 1 0.9192 0.9171 0.9073 0.9076 0.8975 0.8946 0.4672
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+ 35 HGR0000144_T2 B2_HGR0000144_T2 B2 HTO1 6257 792 1 0.9100 0.9092 0.9107 0.9097 0.8845 0.8826 0.1124
25
+ 37 HGR0000395_T0 B2_HGR0000395_T0 B2 HTO3 2786 1149 0 0.9209 0.9200 NaN NaN 0.8953 NaN 0.2920
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+ 38 HGR0000418_T1 B2_HGR0000418_T1 B2 HTO1 6151 314 0 0.9159 0.9156 NaN NaN 0.8813 NaN 0.0486
27
+ 39 SHD2_HC B2_SHD2_HC B2 HTO3 3484 2152 0 0.9169 0.9156 NaN NaN 0.9051 NaN 0.3818
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+ 44 HGR0000051_T2 B3_HGR0000051_T2 B3 HTO5 2109 1961 3 0.9107 0.9183 0.9019 0.9107 0.9088 0.9036 0.4818
29
+ 46 HGR0000101_T0 B3_HGR0000101_T0 B3 HTO5 920 961 2 0.9206 0.9198 0.9190 0.9162 0.9035 0.8970 0.5109
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+ 52 HGR0000134_T1 B3_HGR0000134_T1 B3 HTO5 2705 3488 1 0.9228 0.9245 0.9205 0.9195 0.9125 0.9043 0.5632
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+ 55 HGR0000142_T0 B3_HGR0000142_T0 B3 HTO5 2766 2127 0 0.9226 0.9222 NaN NaN 0.9004 NaN 0.4347
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+ 57 HGR0000392_T3 B3_HGR0000392_T3 B3 HTO5 1413 3297 1 0.9163 0.9174 0.9144 0.9117 0.9103 0.9022 0.7000
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+ 60 HGR0000430_T1 B3_HGR0000430_T1 B3 HTO5 1875 1390 0 0.9223 0.9260 NaN NaN 0.9058 NaN 0.4257
34
+ 64 SHD6_HC B3_SHD6_HC B3 HTO5 2487 2909 0 0.9165 0.9146 NaN NaN 0.9054 NaN 0.5391
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/8707931c36a42f54/prepare.log ADDED
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+ 2026-10-02T21:22:49+09:00 launch prepare MemAvailable 103 GiB
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+ {
3
+ "0": {
4
+ "test": 11,
5
+ "train": 43,
6
+ "inner_val": 4,
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+ "test_groups": {
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+ "COVID": 8,
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+ "HC": 3
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+ },
11
+ "alpha_genes_estimated": 10928
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+ },
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+ "1": {
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+ "test": 12,
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+ "train": 41,
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+ "inner_val": 5,
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+ "test_groups": {
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+ "COVID": 10,
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+ "HC": 2
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+ },
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+ "alpha_genes_estimated": 10883
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+ },
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+ "2": {
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+ "test": 13,
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+ "train": 41,
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+ "inner_val": 4,
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+ "test_groups": {
28
+ "COVID": 11,
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+ "HC": 2
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+ },
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+ "alpha_genes_estimated": 10888
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+ },
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+ "3": {
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+ "test": 10,
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+ "train": 45,
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+ "inner_val": 3,
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+ "test_groups": {
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+ "COVID": 8,
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+ "HC": 2
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+ },
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+ "alpha_genes_estimated": 10925
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+ },
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+ "4": {
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+ "test": 12,
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+ "train": 42,
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+ "inner_val": 4,
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+ "test_groups": {
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+ "COVID": 10,
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+ "HC": 2
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+ },
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+ "alpha_genes_estimated": 10915
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+ }
53
+ } {}
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/919f79a25e62b30c/rds.log ADDED
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+ 2026-10-02T21:06:54+09:00 launch rds MemAvailable 100 GiB
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+ 21:06:56 reading /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/GSE161918/raw/GSE161918_AllBatches_SeuratObj.rds.gz
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+ 21:08:01 read done; class Seurat ; mem 18.4 Gb
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+ used (Mb) gc trigger (Mb) max used (Mb)
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+ Ncells 4596844 245.5 7132770 381 7132770 381.0
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+ Vcells 2424682769 18498.9 3974886648 30326 2470401169 18847.7
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+ 21:08:02 meta.data 411902 x 94
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+ 21:08:22 counts 32738 x 411902 nnz 634566818 integer TRUE
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+ used (Mb) gc trigger (Mb) max used (Mb)
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+ Ncells 4607642 246.1 7132770 381 7132770 381.0
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+ Vcells 2425333364 18503.9 3974886648 30326 3847280901 29352.5
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+ 21:08:39 done in 102 s
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/dependency/e2ebdf8a70b58cfd/pairing.log ADDED
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+ 2026-10-02T21:15:53+09:00 launch pairing MemAvailable 103 GiB
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+ {"t": "2026-10-02T12:16:01.322797+00:00", "stage": "pairing", "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_id_match": {"exact_subject_timepoint": 63, "subject_timepoint; bulk column name corrected": 1, "subject_timepoint; GEO bulk timepoint characteristic differs": 1}, "hto_check": {"selected_cells": 224919, "timepoint_agrees_selected": 224919}}