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single-cell-rna-seq
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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_imperial_eskd_cv2_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_imperial_eskd_cv3.log +80 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_imperial_eskd_cv3_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_imperial_eskd_cv4.log +80 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_imperial_eskd_cv2_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 17063 genes; mixture 29 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 = 1
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-07 02:59:52.378994
44
+ Estimated time to complete: 27mins
45
+ Estimated finishing time: 2026-10-07 03:26:15.738994
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 03:10:56.084641
62
+ Estimated time to complete: 10mins
63
+ Estimated finishing time: 2026-10-07 03:20:18.004641
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: 29 x 17062 x 6
78
+ genes used after the outlier filter: 17062
79
+ elapsed min: 16.92
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/imperial_eskd/cv2_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_imperial_eskd_cv3.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 5831 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 = 5
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-06 20:24:17.321719
44
+ Estimated time to complete: 9mins
45
+ Estimated finishing time: 2026-10-06 20:32:54.041719
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 20:27:47.209309
62
+ Estimated time to complete: 5mins
63
+ Estimated finishing time: 2026-10-06 20:32:13.609309
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 5826 x 6
78
+ genes used after the outlier filter: 5826
79
+ elapsed min: 5.43
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/imperial_eskd/cv3
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_imperial_eskd_cv3_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 17087 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 = 1
40
+ Aligning reference and mixture...
41
+ Normalizing reference...
42
+ Run Gibbs sampling...
43
+ Current time: 2026-10-07 03:16:54.582993
44
+ Estimated time to complete: 21mins
45
+ Estimated finishing time: 2026-10-07 03:36:58.662993
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 03:25:37.677159
62
+ Estimated time to complete: 9mins
63
+ Estimated finishing time: 2026-10-07 03:34:11.997159
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 17086 x 6
78
+ genes used after the outlier filter: 17086
79
+ elapsed min: 13.5
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/imperial_eskd/cv3_full
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/bp_imperial_eskd_cv4.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 5824 genes; mixture 32 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: 2026-10-06 20:29:49.272153
44
+ Estimated time to complete: 11mins
45
+ Estimated finishing time: 2026-10-06 20:40:40.792153
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 20:34:57.292756
62
+ Estimated time to complete: 6mins
63
+ Estimated finishing time: 2026-10-06 20:40:55.052756
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: 32 x 5818 x 6
78
+ genes used after the outlier filter: 5818
79
+ elapsed min: 7.34
80
+ BAYESPRISM_OK /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/bayesprism_paired_20261006/inputs/imperial_eskd/cv4