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  1. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ye2026_sepsis_fewshot4_full.log +78 -0
  2. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_FA_20261007T130133.log +60 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_FB_20261007T130133.log +40 -0
  4. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_HA_20261008T022130.log +52 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ye2026_sepsis_fewshot4_full.log ADDED
@@ -0,0 +1,78 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ Warning messages:
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+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
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+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
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+ reference 28 states x 16072 genes; mixture 77 samples; cores 4
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+ number of cells in each cell state
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+ cell.state.labels
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+ B cell|Effector B cell B cell|Memory B cell
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+ 1 1
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+ B cell|Naive B cell B cell|Plasma cell
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+ 1 1
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+ B cell|Transitional B cell DC|cDC2
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+ 1 1
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+ DC|minor DC|pDC
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+ 1 1
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+ Monocyte|CD14 monocyte Monocyte|CD16 monocyte
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+ 1 1
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+ Monocyte|Intermediate monocyte NK cell|CD56bright NK cell
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+ 1 1
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+ NK cell|CD56dim NK cell NK cell|Proliferating NK cell
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+ 1 1
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+ Other|Erythrocyte Other|ILC
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+ 1 1
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+ Other|Platelet Other|Progenitor cell
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+ 1 1
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+ T cell|CD8aa T cell|DN T cell
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+ 1 1
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+ T cell|gdT T cell|MAIT
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+ 1 1
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+ T cell|Memory CD4 T cell T cell|Memory CD8 T cell
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+ 1 1
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+ T cell|Naive CD4 T cell T cell|Naive CD8 T cell
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+ 1 1
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+ T cell|Proliferating T cell T cell|Treg
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+ 1 1
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+ recommend to have sufficient number of cells in each cell state
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+ No tumor reference is speficied. Reference cell types are treated equally.
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+ Number of outlier genes filtered from mixture = 2
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+ Aligning reference and mixture...
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+ Normalizing reference...
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+ Run Gibbs sampling...
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+ Current time: 2026-10-06 22:54:12.032859
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+ Estimated time to complete: 1hrs 32mins
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+ Estimated finishing time: 2026-10-07 00:25:24.032859
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+ Start run...
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+ R Version: R version 4.5.2 (2025-10-31)
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+
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+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
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+
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+
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+ Stopping cluster
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+
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+ Update the reference matrix ...
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+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
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+
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+
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+ Stopping cluster
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+
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+ Run Gibbs sampling using updated reference ...
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+ Current time: 2026-10-06 23:21:53.855828
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+ Estimated time to complete: 26mins
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+ Estimated finishing time: 2026-10-06 23:47:34.655828
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+ Start run...
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+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
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+
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+
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+ Stopping cluster
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+
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+ Warning messages:
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+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
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+ Unknown option on commandline: --file
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+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
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+ Unknown option on commandline: --file
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+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
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+ Unknown option on commandline: --file
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+ Z dims: 77 x 16070 x 6
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+ genes used after the outlier filter: 16070
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+ elapsed min: 40.05
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+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/ye2026_sepsis/fewshot4_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_FA_20261007T130133.log ADDED
@@ -0,0 +1,60 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ 2026-10-07T13:01:33 lane FA: 4 cores, steps fractions, cohorts imperial_eskd ji2025_chili giroux2022
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+ 2026-10-07T13:01:33 --- fractions imperial_eskd fewshot0
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+ 2026-10-07T13:59:21 fractions imperial_eskd fewshot0: 3468 s
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+ 2026-10-07T13:59:21 --- fractions imperial_eskd fewshot1
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+ 2026-10-07T14:52:41 fractions imperial_eskd fewshot1: 3200 s
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+ 2026-10-07T14:52:41 --- fractions imperial_eskd fewshot2
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+ 2026-10-07T15:50:24 fractions imperial_eskd fewshot2: 3463 s
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+ 2026-10-07T15:50:24 --- fractions imperial_eskd fewshot3
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+ 2026-10-07T16:45:47 fractions imperial_eskd fewshot3: 3323 s
10
+ 2026-10-07T16:45:47 --- fractions imperial_eskd fewshot4
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+ 2026-10-07T17:40:59 fractions imperial_eskd fewshot4: 3312 s
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+ 2026-10-07T17:40:59 --- fractions imperial_eskd cv0
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+ 2026-10-07T18:13:00 fractions imperial_eskd cv0: 1921 s
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+ 2026-10-07T18:13:00 --- fractions imperial_eskd cv1
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+ 2026-10-07T18:38:30 fractions imperial_eskd cv1: 1530 s
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+ 2026-10-07T18:38:30 --- fractions imperial_eskd cv2
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+ 2026-10-07T19:04:06 fractions imperial_eskd cv2: 1536 s
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+ 2026-10-07T19:04:06 --- fractions imperial_eskd cv3
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+ 2026-10-07T19:31:02 fractions imperial_eskd cv3: 1616 s
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+ 2026-10-07T19:31:02 --- fractions imperial_eskd cv4
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+ 2026-10-07T19:57:15 fractions imperial_eskd cv4: 1573 s
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+ 2026-10-07T19:57:15 --- fractions ji2025_chili fewshot0
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+ 2026-10-07T20:22:16 fractions ji2025_chili fewshot0: 1501 s
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+ 2026-10-07T20:22:16 --- fractions ji2025_chili fewshot1
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+ 2026-10-07T20:45:57 fractions ji2025_chili fewshot1: 1421 s
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+ 2026-10-07T20:45:57 --- fractions ji2025_chili fewshot2
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+ 2026-10-07T21:09:40 fractions ji2025_chili fewshot2: 1423 s
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+ 2026-10-07T21:09:40 --- fractions ji2025_chili fewshot3
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+ 2026-10-07T21:33:26 fractions ji2025_chili fewshot3: 1426 s
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+ 2026-10-07T21:33:26 --- fractions ji2025_chili fewshot4
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+ 2026-10-07T21:59:05 fractions ji2025_chili fewshot4: 1539 s
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+ 2026-10-07T21:59:05 --- fractions ji2025_chili cv0
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+ 2026-10-07T22:20:48 fractions ji2025_chili cv0: 1303 s
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+ 2026-10-07T22:20:48 --- fractions ji2025_chili cv1
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+ 2026-10-07T22:41:22 fractions ji2025_chili cv1: 1234 s
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+ 2026-10-07T22:41:22 --- fractions ji2025_chili cv2
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+ 2026-10-07T23:03:01 fractions ji2025_chili cv2: 1299 s
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+ 2026-10-07T23:03:01 --- fractions ji2025_chili cv3
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+ 2026-10-07T23:21:49 fractions ji2025_chili cv3: 1128 s
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+ 2026-10-07T23:21:49 --- fractions ji2025_chili cv4
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+ 2026-10-07T23:41:57 fractions ji2025_chili cv4: 1208 s
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+ 2026-10-07T23:41:57 --- fractions giroux2022 fewshot0
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+ 2026-10-07T23:59:48 fractions giroux2022 fewshot0: 1071 s
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+ 2026-10-07T23:59:48 --- fractions giroux2022 fewshot1
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+ 2026-10-08T00:17:44 fractions giroux2022 fewshot1: 1076 s
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+ 2026-10-08T00:17:44 --- fractions giroux2022 fewshot2
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+ 2026-10-08T00:35:56 fractions giroux2022 fewshot2: 1092 s
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+ 2026-10-08T00:35:56 --- fractions giroux2022 fewshot3
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+ 2026-10-08T00:54:06 fractions giroux2022 fewshot3: 1090 s
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+ 2026-10-08T00:54:06 --- fractions giroux2022 fewshot4
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+ 2026-10-08T01:12:32 fractions giroux2022 fewshot4: 1106 s
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+ 2026-10-08T01:12:32 --- fractions giroux2022 cv1
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+ 2026-10-08T01:29:37 fractions giroux2022 cv1: 1025 s
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+ 2026-10-08T01:29:37 --- fractions giroux2022 cv2
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+ 2026-10-08T01:46:18 fractions giroux2022 cv2: 1001 s
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+ 2026-10-08T01:46:18 --- fractions giroux2022 cv3
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+ 2026-10-08T02:03:23 fractions giroux2022 cv3: 1025 s
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+ 2026-10-08T02:03:23 --- fractions giroux2022 cv4
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+ 2026-10-08T02:20:22 fractions giroux2022 cv4: 1019 s
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+ 2026-10-08T02:20:22 lane FA finished; failed=0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_FB_20261007T130133.log ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 2026-10-07T13:01:33 lane FB: 4 cores, steps fractions, cohorts ye2026_sepsis immicro
2
+ 2026-10-07T13:01:33 --- fractions ye2026_sepsis fewshot1
3
+ 2026-10-07T13:41:22 fractions ye2026_sepsis fewshot1: 2389 s
4
+ 2026-10-07T13:41:22 --- fractions ye2026_sepsis fewshot2
5
+ 2026-10-07T14:22:20 fractions ye2026_sepsis fewshot2: 2458 s
6
+ 2026-10-07T14:22:20 --- fractions ye2026_sepsis fewshot3
7
+ 2026-10-07T15:02:35 fractions ye2026_sepsis fewshot3: 2415 s
8
+ 2026-10-07T15:02:35 --- fractions ye2026_sepsis fewshot4
9
+ 2026-10-07T15:43:15 fractions ye2026_sepsis fewshot4: 2440 s
10
+ 2026-10-07T15:43:15 --- fractions ye2026_sepsis cv0
11
+ 2026-10-07T16:06:15 fractions ye2026_sepsis cv0: 1380 s
12
+ 2026-10-07T16:06:15 --- fractions ye2026_sepsis cv1
13
+ 2026-10-07T16:30:10 fractions ye2026_sepsis cv1: 1435 s
14
+ 2026-10-07T16:30:10 --- fractions ye2026_sepsis cv2
15
+ 2026-10-07T16:52:34 fractions ye2026_sepsis cv2: 1344 s
16
+ 2026-10-07T16:52:34 --- fractions ye2026_sepsis cv3
17
+ 2026-10-07T17:15:49 fractions ye2026_sepsis cv3: 1395 s
18
+ 2026-10-07T17:15:49 --- fractions ye2026_sepsis cv4
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+ 2026-10-07T17:38:40 fractions ye2026_sepsis cv4: 1371 s
20
+ 2026-10-07T17:38:40 --- fractions immicro fewshot0
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+ 2026-10-07T18:16:35 fractions immicro fewshot0: 2275 s
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+ 2026-10-07T18:16:35 --- fractions immicro fewshot1
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+ 2026-10-07T18:57:36 fractions immicro fewshot1: 2461 s
24
+ 2026-10-07T18:57:36 --- fractions immicro fewshot2
25
+ 2026-10-07T19:34:55 fractions immicro fewshot2: 2239 s
26
+ 2026-10-07T19:34:55 --- fractions immicro fewshot3
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+ 2026-10-07T20:15:24 fractions immicro fewshot3: 2429 s
28
+ 2026-10-07T20:15:24 --- fractions immicro fewshot4
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+ 2026-10-07T20:51:29 fractions immicro fewshot4: 2165 s
30
+ 2026-10-07T20:51:29 --- fractions immicro cv0
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+ 2026-10-07T21:13:34 fractions immicro cv0: 1325 s
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+ 2026-10-07T21:13:34 --- fractions immicro cv1
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+ 2026-10-07T21:34:55 fractions immicro cv1: 1281 s
34
+ 2026-10-07T21:34:55 --- fractions immicro cv2
35
+ 2026-10-07T21:56:19 fractions immicro cv2: 1284 s
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+ 2026-10-07T21:56:19 --- fractions immicro cv3
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+ 2026-10-07T22:17:37 fractions immicro cv3: 1278 s
38
+ 2026-10-07T22:17:37 --- fractions immicro cv4
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+ 2026-10-07T22:40:41 fractions immicro cv4: 1384 s
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+ 2026-10-07T22:40:41 lane FB finished; failed=0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_HA_20261008T022130.log ADDED
@@ -0,0 +1,52 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ 2026-10-08T02:21:30 lane HA: 4 cores, steps hires, cohorts imperial_eskd ji2025_chili giroux2022
2
+ 2026-10-08T02:21:31 --- hires imperial_eskd fewshot0
3
+ 2026-10-08T02:59:55 hires imperial_eskd fewshot0: 2304 s
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+ 2026-10-08T02:59:56 --- hires imperial_eskd fewshot1
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+ 2026-10-08T03:38:55 hires imperial_eskd fewshot1: 2339 s
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+ 2026-10-08T03:38:56 --- hires imperial_eskd fewshot2
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+ 2026-10-08T04:17:26 hires imperial_eskd fewshot2: 2310 s
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+ 2026-10-08T04:17:27 --- hires imperial_eskd fewshot3
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+ 2026-10-08T04:57:13 hires imperial_eskd fewshot3: 2386 s
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+ 2026-10-08T04:57:13 --- hires imperial_eskd fewshot4
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+ 2026-10-08T05:36:26 hires imperial_eskd fewshot4: 2353 s
12
+ 2026-10-08T05:36:26 --- hires imperial_eskd cv0
13
+ 2026-10-08T05:47:09 hires imperial_eskd cv0: 643 s
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+ 2026-10-08T05:47:09 --- hires imperial_eskd cv1
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+ 2026-10-08T05:53:23 hires imperial_eskd cv1: 374 s
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+ 2026-10-08T05:53:23 --- hires imperial_eskd cv2
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+ 2026-10-08T06:00:12 hires imperial_eskd cv2: 409 s
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+ 2026-10-08T06:00:12 --- hires imperial_eskd cv3
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+ 2026-10-08T06:06:13 hires imperial_eskd cv3: 361 s
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+ 2026-10-08T06:06:13 --- hires imperial_eskd cv4
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+ 2026-10-08T06:13:42 hires imperial_eskd cv4: 449 s
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+ 2026-10-08T06:13:43 --- hires ji2025_chili fewshot0
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+ 2026-10-08T06:17:56 hires ji2025_chili fewshot0: 253 s
24
+ 2026-10-08T06:17:56 --- hires ji2025_chili fewshot1
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+ 2026-10-08T06:22:41 hires ji2025_chili fewshot1: 285 s
26
+ 2026-10-08T06:22:41 --- hires ji2025_chili fewshot2
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+ 2026-10-08T06:26:56 hires ji2025_chili fewshot2: 255 s
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+ 2026-10-08T06:26:57 --- hires ji2025_chili fewshot3
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+ 2026-10-08T06:30:36 hires ji2025_chili fewshot3: 219 s
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+ 2026-10-08T06:30:36 --- hires ji2025_chili fewshot4
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+ 2026-10-08T06:34:37 hires ji2025_chili fewshot4: 241 s
32
+ 2026-10-08T06:34:37 skip hires ji2025_chili cv0: 7 samples (HiRes needs more samples than cell types)
33
+ 2026-10-08T06:34:37 skip hires ji2025_chili cv1: 6 samples (HiRes needs more samples than cell types)
34
+ 2026-10-08T06:34:37 skip hires ji2025_chili cv2: 6 samples (HiRes needs more samples than cell types)
35
+ 2026-10-08T06:34:37 skip hires ji2025_chili cv3: 8 samples (HiRes needs more samples than cell types)
36
+ 2026-10-08T06:34:37 skip hires ji2025_chili cv4: 6 samples (HiRes needs more samples than cell types)
37
+ 2026-10-08T06:34:37 --- hires giroux2022 fewshot0
38
+ 2026-10-08T06:36:48 hires giroux2022 fewshot0: 131 s
39
+ 2026-10-08T06:36:48 --- hires giroux2022 fewshot1
40
+ 2026-10-08T06:38:37 hires giroux2022 fewshot1: 109 s
41
+ 2026-10-08T06:38:38 --- hires giroux2022 fewshot2
42
+ 2026-10-08T06:41:07 hires giroux2022 fewshot2: 149 s
43
+ 2026-10-08T06:41:07 --- hires giroux2022 fewshot3
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+ 2026-10-08T06:43:50 hires giroux2022 fewshot3: 163 s
45
+ 2026-10-08T06:43:50 --- hires giroux2022 fewshot4
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+ 2026-10-08T06:45:38 hires giroux2022 fewshot4: 108 s
47
+ 2026-10-08T06:45:38 skip hires giroux2022 cv0: 4 samples (HiRes needs more samples than cell types)
48
+ 2026-10-08T06:45:38 skip hires giroux2022 cv1: 5 samples (HiRes needs more samples than cell types)
49
+ 2026-10-08T06:45:38 skip hires giroux2022 cv2: 6 samples (HiRes needs more samples than cell types)
50
+ 2026-10-08T06:45:38 skip hires giroux2022 cv3: 6 samples (HiRes needs more samples than cell types)
51
+ 2026-10-08T06:45:38 skip hires giroux2022 cv4: 3 samples (HiRes needs more samples than cell types)
52
+ 2026-10-08T06:45:38 lane HA finished; failed=0