Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_cv1.log

@@ -0,0 +1,55 @@
+>Running CIBERSORTxFractions...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] single_cell: TRUE
+>[Options] refsample: refsample.txt
+>[Options] mixture: mixture.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] fraction: 0
+>[Options] replicates: 5
+>[Options] sampling: 0.5
+>[Options] G.min: 300
+>[Options] G.max: 500
+>[Options] q.value: 0.01
+>[Options] perm: 0
+>[Options] QN: FALSE
+>[Options] verbose: TRUE
+>Making reference sample file.
+>Making phenotype class file.
+>==========Signature Matrix Settings============
+>Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
+>Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
+>Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
+>Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
+>Q-value for signature matrix construction set to: 0.01
+>Quantile normalization of input samples is disabled
+>===============================================
+>C++14
+>Loaded 30 columns and 19167 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>52137 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 17.5672909918671
+>Best kappa: 17.5672909918671 
+>SVD UpperRightDiag: 75546.6
+>SVD LowerRightDiag: 4300.41
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
+>Enable verbose output
+>Do S-mode batch correction
+>==================CIBERSORTx===================
+>Adjusting mixtures with S-mode batch correction.
+>Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
+>Enable verbose output
+>==================CIBERSORTx===================
+column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
+1 0.12601 0.0327786 0.139898 0.0185195 0.305614 0.37718 9999 16.6667
+2 0.0863573 0.027406 0.169112 0.0586599 0.463835 0.19463 9999 33.3333
+3 0.0284826 0.0506041 0.0861528 0.174771 0.165772 0.494218 9999 50
+4 0.0763762 0.00483459 0.116828 0.0685603 0.569667 0.163733 9999 66.6667
+5 0.0770127 0.0507759 0.0853344 0.101742 0.572851 0.112284 9999 83.3333
+6 0.0810219 0 0.367215 0.0568868 0.266946 0.227931 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_cv2.log

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+>Running CIBERSORTxFractions...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] single_cell: TRUE
+>[Options] refsample: refsample.txt
+>[Options] mixture: mixture.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] fraction: 0
+>[Options] replicates: 5
+>[Options] sampling: 0.5
+>[Options] G.min: 300
+>[Options] G.max: 500
+>[Options] q.value: 0.01
+>[Options] perm: 0
+>[Options] QN: FALSE
+>[Options] verbose: TRUE
+>Making reference sample file.
+>Making phenotype class file.
+>==========Signature Matrix Settings============
+>Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
+>Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
+>Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
+>Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
+>Q-value for signature matrix construction set to: 0.01
+>Quantile normalization of input samples is disabled
+>===============================================
+>C++14
+>Loaded 30 columns and 19167 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51243 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 16.7367001447249
+>Best kappa: 16.7367001447249 
+>SVD UpperRightDiag: 66443.4
+>SVD LowerRightDiag: 3969.92
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
+>Enable verbose output
+>Do S-mode batch correction
+>==================CIBERSORTx===================
+>Adjusting mixtures with S-mode batch correction.
+>Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
+>Enable verbose output
+>==================CIBERSORTx===================
+column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
+1 0.0404701 0 0.231926 0.0719629 0.414588 0.241053 9999 16.6667
+2 0.00502296 0.0271237 0.113551 0.0736937 0.317184 0.463424 9999 33.3333
+3 0 0.064195 0.100732 0.0228621 0.481358 0.330854 9999 50
+4 0 0 0.160729 0.0390495 0.554941 0.245281 9999 66.6667
+5 0 0.0887304 0.162333 0.0250865 0.270755 0.453095 9999 83.3333
+6 0 0.124317 0.120377 0.0448383 0.477252 0.233216 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_cv3.log

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+>Running CIBERSORTxFractions...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] single_cell: TRUE
+>[Options] refsample: refsample.txt
+>[Options] mixture: mixture.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] fraction: 0
+>[Options] replicates: 5
+>[Options] sampling: 0.5
+>[Options] G.min: 300
+>[Options] G.max: 500
+>[Options] q.value: 0.01
+>[Options] perm: 0
+>[Options] QN: FALSE
+>[Options] verbose: TRUE
+>Making reference sample file.
+>Making phenotype class file.
+>==========Signature Matrix Settings============
+>Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
+>Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
+>Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
+>Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
+>Q-value for signature matrix construction set to: 0.01
+>Quantile normalization of input samples is disabled
+>===============================================
+>C++14
+>Loaded 30 columns and 19167 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51918 DEG expressed across 6 samples were identified
+>Group size: 499, Kappa: 16.1529762029382
+>Best kappa: 16.1529762029382 
+>SVD UpperRightDiag: 66222.9
+>SVD LowerRightDiag: 4099.73
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
+>Enable verbose output
+>Do S-mode batch correction
+>==================CIBERSORTx===================
+>Adjusting mixtures with S-mode batch correction.
+>Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
+>Enable verbose output
+>==================CIBERSORTx===================
+column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
+1 0.0295751 0.13086 0.191879 0.0509244 0.0162941 0.580468 9999 12.5
+2 0.0158312 0.0701152 0.209951 0.154255 0.131435 0.418413 9999 25
+3 0 0.29792 0.0377184 0.0836607 0.218236 0.362465 9999 37.5
+4 0 0.298702 0.0818718 0.094496 0.264417 0.260513 9999 50
+5 0.00622381 0.384968 0.00308637 0.0283134 0.239027 0.338382 9999 62.5
+6 0 0.233207 0.0241873 0.0077248 0.509747 0.225134 9999 75
+7 0 0.133959 0.204478 0.0993956 0.249888 0.31228 9999 87.5
+8 0 0.187191 0.0676971 0.167752 0.20664 0.37072 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ji2025_chili_cv4.log

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+>Running CIBERSORTxFractions...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] single_cell: TRUE
+>[Options] refsample: refsample.txt
+>[Options] mixture: mixture.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] fraction: 0
+>[Options] replicates: 5
+>[Options] sampling: 0.5
+>[Options] G.min: 300
+>[Options] G.max: 500
+>[Options] q.value: 0.01
+>[Options] perm: 0
+>[Options] QN: FALSE
+>[Options] verbose: TRUE
+>Making reference sample file.
+>Making phenotype class file.
+>==========Signature Matrix Settings============
+>Pure samples file: /src/outdir//CIBERSORTx_refsample_inferred_refsample.txt
+>Phenotype classes file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.txt
+>Minimum number of DEGs to consider from each phenotype for signature matrix set to: 300
+>Maximum number of DEGs to consider from each phenotype for signature matrix set to: 500
+>Q-value for signature matrix construction set to: 0.01
+>Quantile normalization of input samples is disabled
+>===============================================
+>C++14
+>Loaded 30 columns and 19167 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51720 DEG expressed across 6 samples were identified
+>Group size: 495, Kappa: 10.323168273968
+>Best kappa: 10.323168273968 
+>SVD UpperRightDiag: 42113.4
+>SVD LowerRightDiag: 4079.51
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
+>Enable verbose output
+>Do S-mode batch correction
+>==================CIBERSORTx===================
+>Adjusting mixtures with S-mode batch correction.
+>Running CIBERSORTx on unadjusted mixtures with S-mode adjusted signature matrix.
+>=============CIBERSORTx Settings===============
+>Mixture file: /src/data/mixture.txt
+>Signature matrix file: /src/outdir//CIBERSORTx_sigmatrix_Adjusted.txt
+>Enable verbose output
+>==================CIBERSORTx===================
+column B cell DC Monocyte NK cell Other T cell P-value Correlation RMSE %Completed
+1 0 0.0411428 0.119363 0.0576144 0.739798 0.0420816 9999 16.6667
+2 0 0.0949082 0.141246 0.0671706 0.663886 0.0327894 9999 33.3333
+3 0 0.130282 0.158127 0.0740867 0.342673 0.294832 9999 50
+4 0 0.125932 0.112162 0.0968048 0.386165 0.278937 9999 66.6667
+5 0 0.0522954 0.222496 0.0537005 0.490308 0.1812 9999 83.3333
+6 0 0.0365938 0.0737123 0 0.410012 0.479682 9999 100