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_giroux2022_cv3.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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>45488 DEG expressed across 6 samples were identified
+>Group size: 441, Kappa: 10.9730321323685
+>Best kappa: 10.9730321323685 
+>SVD UpperRightDiag: 61022.7
+>SVD LowerRightDiag: 5561.15
+>=============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 0.0715272 0 0.360551 0.0706575 0.17088 0.326384 9999 16.6667
+2 0.00950486 0 0.255723 0.0378684 0.248898 0.448006 9999 33.3333
+3 0.0114851 0 0.296223 0 0.15085 0.541442 9999 50
+4 0.000238088 0.013145 0.205163 0.100582 0.21959 0.461281 9999 66.6667
+5 0.026247 0 0.24006 0.0138244 0.132197 0.587671 9999 83.3333
+6 0 0.0121627 0.187041 0.0153251 0.0663645 0.719107 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>45472 DEG expressed across 6 samples were identified
+>Group size: 476, Kappa: 11.4353470260573
+>Best kappa: 11.4353470260573 
+>SVD UpperRightDiag: 61706.1
+>SVD LowerRightDiag: 5396.08
+>=============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 0.0248771 0.0342189 0.686032 0.0782877 0.0498911 0.126693 9999 33.3333
+2 0.0372947 0.00596686 0.137567 0.150724 0.174742 0.493705 9999 66.6667
+3 0.0191151 0.00340777 0.179062 0.112858 0.178471 0.507087 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_fewshot0.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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>44576 DEG expressed across 6 samples were identified
+>Group size: 473, Kappa: 17.317148888403
+>Best kappa: 17.317148888403 
+>SVD UpperRightDiag: 60765.8
+>SVD LowerRightDiag: 3509
+>=============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 0.613877 0.0715673 0.269164 0.0453913 9999 9.09091
+2 0.0379761 0.0569227 0.288202 0.116643 0.387473 0.112783 9999 18.1818
+3 0.103089 0 0.132986 0.142964 0.184263 0.436698 9999 27.2727
+4 0.13885 0 0.131833 0.0914099 0.230181 0.407726 9999 36.3636
+5 0.118089 0 0.211959 0.0661594 0.212826 0.390967 9999 45.4545
+6 0.136189 0.0191932 0.240592 0.0339075 0.286949 0.28317 9999 54.5455
+7 0.0583118 0 0.174581 0.0643641 0.402502 0.30024 9999 63.6364
+8 0.047538 0 0.220469 0 0.277898 0.454094 9999 72.7273
+9 0.0094689 0.00098994 0.599315 0.0190605 0.169692 0.201474 9999 81.8182
+10 0.0967381 0 0.162885 0 0.224153 0.516224 9999 90.9091
+11 0.112809 0 0.126006 0.00953858 0.228032 0.523615 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_fewshot1.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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>44028 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 12.651438468517
+>Best kappa: 12.651438468517 
+>SVD UpperRightDiag: 63334.9
+>SVD LowerRightDiag: 5006.14
+>=============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 0.623057 0.0698763 0.136615 0.170451 9999 10
+2 0.0230168 0.0642763 0.297856 0.134569 0.254873 0.225409 9999 20
+3 0 0.0402428 0.346901 0.0475309 0.174035 0.39129 9999 30
+4 0.0885935 0 0.382776 0.111819 0.202551 0.21426 9999 40
+5 0.0234636 0.0210135 0.208531 0.0144696 0.18536 0.547162 9999 50
+6 0.0368853 0.0167927 0.116722 0.0549775 0.170356 0.604266 9999 60
+7 0.0133291 0.0180791 0.213117 0 0.152111 0.603363 9999 70
+8 0.00894354 0.00242072 0.613343 0.0199502 0.109446 0.245896 9999 80
+9 0.0755071 0 0.172581 0.00410781 0.107835 0.639969 9999 90
+10 0.110917 0 0.146089 0.0181959 0.11474 0.610058 9999 100