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  1. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_fewshot4.log +73 -0
  2. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv0.log +66 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv1.log +66 -0
  4. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv2.log +65 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_fewshot4.log ADDED
@@ -0,0 +1,73 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ >Running CIBERSORTxFractions...
2
+ >[Options] username: [REDACTED]
3
+ >[Options] token: [REDACTED]
4
+ >[Options] single_cell: TRUE
5
+ >[Options] refsample: refsample.txt
6
+ >[Options] mixture: mixture.txt
7
+ >[Options] rmbatchSmode: TRUE
8
+ >[Options] fraction: 0
9
+ >[Options] replicates: 5
10
+ >[Options] sampling: 0.5
11
+ >[Options] G.min: 300
12
+ >[Options] G.max: 500
13
+ >[Options] q.value: 0.01
14
+ >[Options] perm: 0
15
+ >[Options] QN: FALSE
16
+ >[Options] verbose: TRUE
17
+ >Making reference sample file.
18
+ >Making phenotype class file.
19
+ >==========Signature Matrix Settings============
20
+ >Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
21
+ >Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
22
+ >Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
23
+ >Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
24
+ >Q-value for signature matrix construction set to: 0.01
25
+ >Quantile normalization of input samples is disabled
26
+ >===============================================
27
+ >C++14
28
+ >Loaded 30 columns and 19167 rows
29
+ >=============Make Signature Matrix=============
30
+ >Maximum condition number (kappa):999
31
+ >49221 DEG expressed across 6 samples were identified
32
+ >Group size: 500, Kappa: 8.8817857102621
33
+ >Best kappa: 8.8817857102621
34
+ >SVD UpperRightDiag: 37004.9
35
+ >SVD LowerRightDiag: 4166.38
36
+ >=============CIBERSORTx Settings===============
37
+ >Mixture file: /src/data/mixture.txt
38
+ >Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
39
+ >Enable verbose output
40
+ >Do S-mode batch correction
41
+ >==================CIBERSORTx===================
42
+ >Adjusting mixtures with S-mode batch correction.
43
+ >Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
44
+ >=============CIBERSORTx Settings===============
45
+ >Mixture file: /src/data/mixture.txt
46
+ >Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
47
+ >Enable verbose output
48
+ >==================CIBERSORTx===================
49
+ column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
50
+ 1 0.176062 0.170818 0.139661 0.00236117 0.130489 0.380608 9999 4.16667
51
+ 2 0.0842802 0.0614801 0.194191 0.0780196 0.260065 0.321964 9999 8.33333
52
+ 3 0.0942613 0.0413219 0.260914 0.0860985 0.278976 0.238428 9999 12.5
53
+ 4 0.184296 0.0446817 0.308976 0.0952053 0.296916 0.0699254 9999 16.6667
54
+ 5 0.103663 0 0.455219 0.0404345 0.246482 0.154202 9999 20.8333
55
+ 6 0.155489 0 0.537717 0.00514263 0.0839948 0.217657 9999 25
56
+ 7 0.135944 0.0561472 0.355953 0.0227686 0.391988 0.0371996 9999 29.1667
57
+ 8 0.100634 0.183155 0.382719 0.0306772 0.29724 0.00557466 9999 33.3333
58
+ 9 0.126729 0.14137 0.343626 0 0.0991616 0.289113 9999 37.5
59
+ 10 0.0928593 0.209889 0.301599 0.00489504 0.104077 0.28668 9999 41.6667
60
+ 11 0.0294836 0 0.553729 0.0238771 0.115038 0.277872 9999 45.8333
61
+ 12 0.0267615 0.100653 0.141391 0.033068 0.332455 0.365672 9999 50
62
+ 13 0.03077 0.0189953 0.246229 0 0.0569662 0.647039 9999 54.1667
63
+ 14 0.0233388 0.215366 0.127907 0.0191219 0.194598 0.419668 9999 58.3333
64
+ 15 0.071468 0.0930764 0.287726 0.0587813 0.17021 0.318738 9999 62.5
65
+ 16 0.120373 0.0142216 0.388187 0.0420431 0.160816 0.274359 9999 66.6667
66
+ 17 0.212815 0.0546567 0.4604 0.0324716 0.108129 0.131527 9999 70.8333
67
+ 18 0.130151 0.222732 0.13054 0.0287978 0.129989 0.357789 9999 75
68
+ 19 0.0809963 0.166357 0.100663 0.0344504 0.185143 0.43239 9999 79.1667
69
+ 20 0.0390075 0 0.348979 0.0798346 0.214113 0.318066 9999 83.3333
70
+ 21 0.0182285 0.0644923 0.147334 0.165445 0.12385 0.480649 9999 87.5
71
+ 22 0.0741464 0.080281 0.238307 0.0976696 0.301975 0.207621 9999 91.6667
72
+ 23 0.112182 0.1315 0.199474 0.0934478 0.24933 0.214066 9999 95.8333
73
+ 24 0.0843584 0 0.469674 0.0842056 0.191251 0.170512 9999 100
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv0.log ADDED
@@ -0,0 +1,66 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ >Running CIBERSORTxFractions...
2
+ >[Options] username: [REDACTED]
3
+ >[Options] token: [REDACTED]
4
+ >[Options] single_cell: TRUE
5
+ >[Options] refsample: refsample.txt
6
+ >[Options] mixture: mixture.txt
7
+ >[Options] rmbatchSmode: TRUE
8
+ >[Options] fraction: 0
9
+ >[Options] replicates: 5
10
+ >[Options] sampling: 0.5
11
+ >[Options] G.min: 300
12
+ >[Options] G.max: 500
13
+ >[Options] q.value: 0.01
14
+ >[Options] perm: 0
15
+ >[Options] QN: FALSE
16
+ >[Options] verbose: TRUE
17
+ >Making reference sample file.
18
+ >Making phenotype class file.
19
+ >==========Signature Matrix Settings============
20
+ >Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
21
+ >Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
22
+ >Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
23
+ >Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
24
+ >Q-value for signature matrix construction set to: 0.01
25
+ >Quantile normalization of input samples is disabled
26
+ >===============================================
27
+ >C++14
28
+ >Loaded 30 columns and 19864 rows
29
+ >=============Make Signature Matrix=============
30
+ >Maximum condition number (kappa):999
31
+ >52028 DEG expressed across 6 samples were identified
32
+ >Group size: 500, Kappa: 28.748669174394
33
+ >Best kappa: 28.748669174394
34
+ >SVD UpperRightDiag: 110560
35
+ >SVD LowerRightDiag: 3845.76
36
+ >=============CIBERSORTx Settings===============
37
+ >Mixture file: /src/data/mixture.txt
38
+ >Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
39
+ >Enable verbose output
40
+ >Do S-mode batch correction
41
+ >==================CIBERSORTx===================
42
+ >Adjusting mixtures with S-mode batch correction.
43
+ >Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
44
+ >=============CIBERSORTx Settings===============
45
+ >Mixture file: /src/data/mixture.txt
46
+ >Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
47
+ >Enable verbose output
48
+ >==================CIBERSORTx===================
49
+ column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
50
+ 1 0.0772717 0.259628 0.0992794 0.0681464 0.0738841 0.42179 9999 5.88235
51
+ 2 0.272459 0 0.109503 0 0.298801 0.319237 9999 11.7647
52
+ 3 0 0.329654 0.192528 0.0987969 0.235142 0.143879 9999 17.6471
53
+ 4 0.0263172 0.149729 0.339081 0.088618 0.259725 0.13653 9999 23.5294
54
+ 5 0.199974 0.0289728 0.0205444 0 0.00350011 0.747009 9999 29.4118
55
+ 6 0.0656272 0.16731 0.362536 0.190348 0.0727695 0.14141 9999 35.2941
56
+ 7 0.0164348 0.398169 0 0.0937174 0.0100321 0.481647 9999 41.1765
57
+ 8 0 0.401328 0 0.336935 0.0132156 0.248521 9999 47.0588
58
+ 9 0.0838898 0.221521 0.126188 0 0.0875944 0.480807 9999 52.9412
59
+ 10 0.20453 0.0933973 0 0.0105491 0 0.691523 9999 58.8235
60
+ 11 0.0102802 0.268455 0.262322 0 0.0273264 0.431617 9999 64.7059
61
+ 12 0.413874 0.0165607 0.0531148 0 0.00104751 0.515403 9999 70.5882
62
+ 13 0 0.229483 0.244836 0.334555 0.00282725 0.188299 9999 76.4706
63
+ 14 0.0819009 0.0533682 0.197613 0.111221 0.103897 0.452 9999 82.3529
64
+ 15 0.0400236 0.146649 0.271498 0 0.144038 0.397792 9999 88.2353
65
+ 16 0.157151 0.0755886 0.260556 0.0391869 0.213026 0.254491 9999 94.1176
66
+ 17 0.138035 0.167303 0.0466769 0.0067753 0.0231733 0.618036 9999 100
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv1.log ADDED
@@ -0,0 +1,66 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ >Running CIBERSORTxFractions...
2
+ >[Options] username: [REDACTED]
3
+ >[Options] token: [REDACTED]
4
+ >[Options] single_cell: TRUE
5
+ >[Options] refsample: refsample.txt
6
+ >[Options] mixture: mixture.txt
7
+ >[Options] rmbatchSmode: TRUE
8
+ >[Options] fraction: 0
9
+ >[Options] replicates: 5
10
+ >[Options] sampling: 0.5
11
+ >[Options] G.min: 300
12
+ >[Options] G.max: 500
13
+ >[Options] q.value: 0.01
14
+ >[Options] perm: 0
15
+ >[Options] QN: FALSE
16
+ >[Options] verbose: TRUE
17
+ >Making reference sample file.
18
+ >Making phenotype class file.
19
+ >==========Signature Matrix Settings============
20
+ >Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
21
+ >Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
22
+ >Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
23
+ >Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
24
+ >Q-value for signature matrix construction set to: 0.01
25
+ >Quantile normalization of input samples is disabled
26
+ >===============================================
27
+ >C++14
28
+ >Loaded 30 columns and 19864 rows
29
+ >=============Make Signature Matrix=============
30
+ >Maximum condition number (kappa):999
31
+ >52778 DEG expressed across 6 samples were identified
32
+ >Group size: 500, Kappa: 28.5479259649129
33
+ >Best kappa: 28.5479259649129
34
+ >SVD UpperRightDiag: 113755
35
+ >SVD LowerRightDiag: 3984.69
36
+ >=============CIBERSORTx Settings===============
37
+ >Mixture file: /src/data/mixture.txt
38
+ >Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
39
+ >Enable verbose output
40
+ >Do S-mode batch correction
41
+ >==================CIBERSORTx===================
42
+ >Adjusting mixtures with S-mode batch correction.
43
+ >Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
44
+ >=============CIBERSORTx Settings===============
45
+ >Mixture file: /src/data/mixture.txt
46
+ >Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
47
+ >Enable verbose output
48
+ >==================CIBERSORTx===================
49
+ column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
50
+ 1 0.0256801 0.0870406 0.0175124 0.271429 0.0110252 0.587313 9999 5.88235
51
+ 2 0.0865785 0.199834 0.316034 0.076733 0.0444153 0.276405 9999 11.7647
52
+ 3 0.0123629 0.295246 0.315556 0.0520229 0.131562 0.19325 9999 17.6471
53
+ 4 0.0870477 0.166716 0 0.235042 0 0.511195 9999 23.5294
54
+ 5 0.0815971 0.182672 0 0.243161 0.00738415 0.485186 9999 29.4118
55
+ 6 0.182292 0.126493 0.34983 0.120963 0.0659272 0.154495 9999 35.2941
56
+ 7 0.203704 0.139773 0.0178761 0.0878434 0.0160956 0.534708 9999 41.1765
57
+ 8 0.229989 0.19976 0.081445 0 0.0107534 0.478052 9999 47.0588
58
+ 9 0.380963 0 0.206292 0 0.0381655 0.37458 9999 52.9412
59
+ 10 0.0168165 0.283798 0.210014 0.0414026 0.00016732 0.447802 9999 58.8235
60
+ 11 0.022671 0.00704047 0.0639554 0 0.180791 0.725542 9999 64.7059
61
+ 12 0.0579999 0.0590988 0.275497 0.202598 0.037619 0.367187 9999 70.5882
62
+ 13 0.0322009 0.119037 0.127708 0.163831 0.183315 0.373908 9999 76.4706
63
+ 14 0.0314842 0.250125 0.39147 0.0446532 0.0190592 0.263209 9999 82.3529
64
+ 15 0.0453576 0.175666 0.238931 0.0923008 0.199414 0.248331 9999 88.2353
65
+ 16 0.172002 0 0.062299 0 0.250582 0.515117 9999 94.1176
66
+ 17 0.261526 0.193502 0.166329 0.0471635 0.0115658 0.319914 9999 100
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv2.log ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ >Running CIBERSORTxFractions...
2
+ >[Options] username: [REDACTED]
3
+ >[Options] token: [REDACTED]
4
+ >[Options] single_cell: TRUE
5
+ >[Options] refsample: refsample.txt
6
+ >[Options] mixture: mixture.txt
7
+ >[Options] rmbatchSmode: TRUE
8
+ >[Options] fraction: 0
9
+ >[Options] replicates: 5
10
+ >[Options] sampling: 0.5
11
+ >[Options] G.min: 300
12
+ >[Options] G.max: 500
13
+ >[Options] q.value: 0.01
14
+ >[Options] perm: 0
15
+ >[Options] QN: FALSE
16
+ >[Options] verbose: TRUE
17
+ >Making reference sample file.
18
+ >Making phenotype class file.
19
+ >==========Signature Matrix Settings============
20
+ >Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
21
+ >Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
22
+ >Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
23
+ >Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
24
+ >Q-value for signature matrix construction set to: 0.01
25
+ >Quantile normalization of input samples is disabled
26
+ >===============================================
27
+ >C++14
28
+ >Loaded 30 columns and 19864 rows
29
+ >=============Make Signature Matrix=============
30
+ >Maximum condition number (kappa):999
31
+ >52065 DEG expressed across 6 samples were identified
32
+ >Group size: 500, Kappa: 33.1777193154457
33
+ >Best kappa: 33.1777193154457
34
+ >SVD UpperRightDiag: 126436
35
+ >SVD LowerRightDiag: 3810.86
36
+ >=============CIBERSORTx Settings===============
37
+ >Mixture file: /src/data/mixture.txt
38
+ >Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
39
+ >Enable verbose output
40
+ >Do S-mode batch correction
41
+ >==================CIBERSORTx===================
42
+ >Adjusting mixtures with S-mode batch correction.
43
+ >Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
44
+ >=============CIBERSORTx Settings===============
45
+ >Mixture file: /src/data/mixture.txt
46
+ >Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
47
+ >Enable verbose output
48
+ >==================CIBERSORTx===================
49
+ column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
50
+ 1 0.0769123 0.246751 0.492016 0.0165502 0.116914 0.0508554 9999 6.25
51
+ 2 0.361201 0.0356112 0.138966 0.0337737 0.254753 0.175696 9999 12.5
52
+ 3 0 0.298148 0.142137 0.0689792 0.102715 0.388022 9999 18.75
53
+ 4 0.175458 0.0587669 0.380163 0.0251828 0.0383912 0.322038 9999 25
54
+ 5 0.0276362 0.255214 0 0.210045 0 0.507105 9999 31.25
55
+ 6 0.121946 0.0871905 0.0676515 0.130892 0.105387 0.486933 9999 37.5
56
+ 7 0.0438018 0.368026 0.171199 0 0.116207 0.300766 9999 43.75
57
+ 8 0.0763387 0.290908 0 0.0351648 0.0169139 0.580675 9999 50
58
+ 9 0.197907 0 0.0798405 0 0 0.722252 9999 56.25
59
+ 10 0.111448 0.101647 0.28727 0 0.0239852 0.47565 9999 62.5
60
+ 11 0.141834 0.160343 0.338337 0.120098 0.208568 0.0308192 9999 68.75
61
+ 12 0.0856207 0.168768 0.055186 0.0352768 0.0979996 0.557149 9999 75
62
+ 13 0.294967 0.0490707 0.0455418 0.0866765 0 0.523744 9999 81.25
63
+ 14 0.118653 0.162697 0.14224 0.0484612 0.0646966 0.463252 9999 87.5
64
+ 15 0 0.349098 0.140414 0.0767698 0.00742236 0.426296 9999 93.75
65
+ 16 0.00978047 0.0235317 0.00538733 0.279581 0.00565527 0.676064 9999 100