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single-cell-rna-seq
bulk-rna-seq
diffusion
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Archive 4 checkpoints (1-4)

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Files changed (4) hide show
  1. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot3_full.log +80 -0
  2. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot4.log +80 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot4_full.log +80 -0
  4. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_pseudocheck.log +158 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot3_full.log ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 29 states x 15802 genes; mixture 25 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|Naive B cell B cell|Plasma cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|ASDC
12
+ 1 1
13
+ DC|cDC2 DC|minor
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|Erythrocyte
22
+ 1 1
23
+ Other|ILC Other|Platelet
24
+ 1 1
25
+ Other|Progenitor cell T cell|CD8aa
26
+ 1 1
27
+ T cell|DN T cell T cell|gdT
28
+ 1 1
29
+ T cell|MAIT T cell|Memory CD4 T cell
30
+ 1 1
31
+ T cell|Memory CD8 T cell T cell|Naive CD4 T cell
32
+ 1 1
33
+ T cell|Naive CD8 T cell T cell|Proliferating T cell
34
+ 1 1
35
+ T cell|Treg
36
+ 1
37
+ recommend to have sufficient number of cells in each cell state
38
+ No tumor reference is speficied. Reference cell types are treated equally.
39
+ Number of outlier genes filtered from mixture = 6
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-07 04:28:05.207356
44
+ Estimated time to complete: 20mins
45
+ Estimated finishing time: 2026-10-07 04:47:33.647356
46
+ Start run...
47
+ R Version: R version 4.5.2 (2025-10-31)
48
+
49
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
50
+
51
+
52
+ Stopping cluster
53
+
54
+ Update the reference matrix ...
55
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
56
+
57
+
58
+ Stopping cluster
59
+
60
+ Run Gibbs sampling using updated reference ...
61
+ Current time: 2026-10-07 04:37:13.801928
62
+ Estimated time to complete: 10mins
63
+ Estimated finishing time: 2026-10-07 04:46:20.921928
64
+ Start run...
65
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
66
+
67
+
68
+ Stopping cluster
69
+
70
+ Warning messages:
71
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
76
+ Unknown option on commandline: --file
77
+ Z dims: 25 x 15796 x 6
78
+ genes used after the outlier filter: 15796
79
+ elapsed min: 13.28
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/ji2025_chili/fewshot3_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot4.log ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 29 states x 5694 genes; mixture 24 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|Naive B cell B cell|Plasma cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|ASDC
12
+ 1 1
13
+ DC|cDC1 DC|cDC2
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|Erythrocyte
22
+ 1 1
23
+ Other|ILC Other|Platelet
24
+ 1 1
25
+ Other|Progenitor cell T cell|CD8aa
26
+ 1 1
27
+ T cell|DN T cell T cell|gdT
28
+ 1 1
29
+ T cell|MAIT T cell|Memory CD4 T cell
30
+ 1 1
31
+ T cell|Memory CD8 T cell T cell|Naive CD4 T cell
32
+ 1 1
33
+ T cell|Naive CD8 T cell T cell|Proliferating T cell
34
+ 1 1
35
+ T cell|Treg
36
+ 1
37
+ recommend to have sufficient number of cells in each cell state
38
+ No tumor reference is speficied. Reference cell types are treated equally.
39
+ Number of outlier genes filtered from mixture = 11
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-06 18:08:26.153597
44
+ Estimated time to complete: 8mins
45
+ Estimated finishing time: 2026-10-06 18:15:46.553597
46
+ Start run...
47
+ R Version: R version 4.5.2 (2025-10-31)
48
+
49
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
50
+
51
+
52
+ Stopping cluster
53
+
54
+ Update the reference matrix ...
55
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
56
+
57
+
58
+ Stopping cluster
59
+
60
+ Run Gibbs sampling using updated reference ...
61
+ Current time: 2026-10-06 18:11:29.308745
62
+ Estimated time to complete: 4mins
63
+ Estimated finishing time: 2026-10-06 18:14:55.468745
64
+ Start run...
65
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
66
+
67
+
68
+ Stopping cluster
69
+
70
+ Warning messages:
71
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
76
+ Unknown option on commandline: --file
77
+ Z dims: 24 x 5683 x 6
78
+ genes used after the outlier filter: 5683
79
+ elapsed min: 4.38
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/ji2025_chili/fewshot4
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_ji2025_chili_fewshot4_full.log ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 29 states x 15934 genes; mixture 24 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|Naive B cell B cell|Plasma cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|ASDC
12
+ 1 1
13
+ DC|cDC1 DC|cDC2
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|Erythrocyte
22
+ 1 1
23
+ Other|ILC Other|Platelet
24
+ 1 1
25
+ Other|Progenitor cell T cell|CD8aa
26
+ 1 1
27
+ T cell|DN T cell T cell|gdT
28
+ 1 1
29
+ T cell|MAIT T cell|Memory CD4 T cell
30
+ 1 1
31
+ T cell|Memory CD8 T cell T cell|Naive CD4 T cell
32
+ 1 1
33
+ T cell|Naive CD8 T cell T cell|Proliferating T cell
34
+ 1 1
35
+ T cell|Treg
36
+ 1
37
+ recommend to have sufficient number of cells in each cell state
38
+ No tumor reference is speficied. Reference cell types are treated equally.
39
+ Number of outlier genes filtered from mixture = 6
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-07 04:41:28.977784
44
+ Estimated time to complete: 19mins
45
+ Estimated finishing time: 2026-10-07 04:59:37.377784
46
+ Start run...
47
+ R Version: R version 4.5.2 (2025-10-31)
48
+
49
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
50
+
51
+
52
+ Stopping cluster
53
+
54
+ Update the reference matrix ...
55
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
56
+
57
+
58
+ Stopping cluster
59
+
60
+ Run Gibbs sampling using updated reference ...
61
+ Current time: 2026-10-07 04:49:04.632364
62
+ Estimated time to complete: 8mins
63
+ Estimated finishing time: 2026-10-07 04:56:46.152364
64
+ Start run...
65
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
66
+
67
+
68
+ Stopping cluster
69
+
70
+ Warning messages:
71
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
76
+ Unknown option on commandline: --file
77
+ Z dims: 24 x 15928 x 6
78
+ genes used after the outlier filter: 15928
79
+ elapsed min: 11.43
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/ji2025_chili/fewshot4_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_pseudocheck.log ADDED
@@ -0,0 +1,158 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ Warning messages:
2
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
3
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
4
+ reference 29 states x 5433 genes; mixture 4 samples; cores 4
5
+ number of cells in each cell state
6
+ cell.state.labels
7
+ B cell|Effector B cell B cell|Memory B cell
8
+ 1 1
9
+ B cell|Naive B cell B cell|Plasma cell
10
+ 1 1
11
+ B cell|Transitional B cell DC|ASDC
12
+ 1 1
13
+ DC|cDC1 DC|cDC2
14
+ 1 1
15
+ DC|pDC Monocyte|CD14 monocyte
16
+ 1 1
17
+ Monocyte|CD16 monocyte Monocyte|Intermediate monocyte
18
+ 1 1
19
+ NK cell|CD56bright NK cell NK cell|CD56dim NK cell
20
+ 1 1
21
+ NK cell|Proliferating NK cell Other|Erythrocyte
22
+ 1 1
23
+ Other|ILC Other|Platelet
24
+ 1 1
25
+ Other|Progenitor cell T cell|CD8aa
26
+ 1 1
27
+ T cell|DN T cell T cell|gdT
28
+ 1 1
29
+ T cell|MAIT T cell|Memory CD4 T cell
30
+ 1 1
31
+ T cell|Memory CD8 T cell T cell|Naive CD4 T cell
32
+ 1 1
33
+ T cell|Naive CD8 T cell T cell|Proliferating T cell
34
+ 1 1
35
+ T cell|Treg
36
+ 1
37
+ recommend to have sufficient number of cells in each cell state
38
+ No tumor reference is speficied. Reference cell types are treated equally.
39
+ Number of outlier genes filtered from mixture = 18
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-06 20:04:20.39824
44
+ Estimated time to complete: 2mins
45
+ Estimated finishing time: 2026-10-06 20:05:32.95824
46
+ Start run...
47
+ R Version: R version 4.5.2 (2025-10-31)
48
+
49
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
50
+
51
+
52
+ Stopping cluster
53
+
54
+ Update the reference matrix ...
55
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
56
+
57
+
58
+ Stopping cluster
59
+
60
+ Run Gibbs sampling using updated reference ...
61
+ Current time: 2026-10-06 20:04:53.794165
62
+ Estimated time to complete: 1mins
63
+ Estimated finishing time: 2026-10-06 20:05:39.914165
64
+ Start run...
65
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
66
+
67
+
68
+ Stopping cluster
69
+
70
+ Warning messages:
71
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
72
+ Unknown option on commandline: --file
73
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
74
+ Unknown option on commandline: --file
75
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
76
+ Unknown option on commandline: --file
77
+ Z dims: 4 x 5415 x 6
78
+ genes used after the outlier filter: 5415
79
+ elapsed min: 0.83
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/giroux2022/cv0_pseudocheck
81
+ Warning messages:
82
+ 1: replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘BayesPrism’
83
+ 2: replacing previous import ‘BiocParallel::register’ by ‘NMF::register’ when loading ‘BayesPrism’
84
+ reference 27 states x 5233 genes; mixture 102 samples; cores 4
85
+ number of cells in each cell state
86
+ cell.state.labels
87
+ B cell|Effector B cell B cell|Memory B cell
88
+ 1 1
89
+ B cell|minor B cell|Naive B cell
90
+ 1 1
91
+ B cell|Transitional B cell DC|cDC2
92
+ 1 1
93
+ DC|minor DC|pDC
94
+ 1 1
95
+ Monocyte|CD14 monocyte Monocyte|CD16 monocyte
96
+ 1 1
97
+ Monocyte|Intermediate monocyte NK cell|CD56bright NK cell
98
+ 1 1
99
+ NK cell|CD56dim NK cell NK cell|Proliferating NK cell
100
+ 1 1
101
+ Other|Erythrocyte Other|ILC
102
+ 1 1
103
+ Other|minor T cell|CD8aa
104
+ 1 1
105
+ T cell|DN T cell T cell|gdT
106
+ 1 1
107
+ T cell|MAIT T cell|Memory CD4 T cell
108
+ 1 1
109
+ T cell|Memory CD8 T cell T cell|minor
110
+ 1 1
111
+ T cell|Naive CD4 T cell T cell|Naive CD8 T cell
112
+ 1 1
113
+ T cell|Treg
114
+ 1
115
+ recommend to have sufficient number of cells in each cell state
116
+ No tumor reference is speficied. Reference cell types are treated equally.
117
+ Number of outlier genes filtered from mixture = 32
118
+ Aligning reference and mixture...
119
+ Normalizing reference...
120
+ Run Gibbs sampling...
121
+ Current time: 2026-10-06 20:05:14.615219
122
+ Estimated time to complete: 29mins
123
+ Estimated finishing time: 2026-10-06 20:33:46.455219
124
+ Start run...
125
+ R Version: R version 4.5.2 (2025-10-31)
126
+
127
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
128
+
129
+
130
+ Stopping cluster
131
+
132
+ Update the reference matrix ...
133
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
134
+
135
+
136
+ Stopping cluster
137
+
138
+ Run Gibbs sampling using updated reference ...
139
+ Current time: 2026-10-06 20:17:47.536543
140
+ Estimated time to complete: 19mins
141
+ Estimated finishing time: 2026-10-06 20:35:56.416543
142
+ Start run...
143
+ snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 4 CPUs.
144
+
145
+
146
+ Stopping cluster
147
+
148
+ Warning messages:
149
+ 1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
150
+ Unknown option on commandline: --file
151
+ 2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
152
+ Unknown option on commandline: --file
153
+ 3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
154
+ Unknown option on commandline: --file
155
+ Z dims: 102 x 5201 x 6
156
+ genes used after the outlier filter: 5201
157
+ elapsed min: 18.22
158
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/immicro/fewshot0_pseudocheck