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_fewshot2.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
+>44711 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 13.9190661056804
+>Best kappa: 13.9190661056804 
+>SVD UpperRightDiag: 57539.6
+>SVD LowerRightDiag: 4133.87
+>=============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 0.00833414 0.125776 0.70366 0.0496668 0.0964122 0.0161508 9999 8.33333
+2 0.0767706 0.0383764 0.175023 0.144835 0.246154 0.318841 9999 16.6667
+3 0.0594688 0.0495378 0.227982 0.0986122 0.23535 0.32905 9999 25
+4 0.141449 0 0.160124 0.100411 0.131114 0.466902 9999 33.3333
+5 0.145105 0 0.173995 0.0580081 0.194768 0.428124 9999 41.6667
+6 0.121468 0 0.252789 0.0321385 0.178714 0.41489 9999 50
+7 0.138466 0.0149452 0.329255 0.0344688 0.247946 0.234918 9999 58.3333
+8 0.054764 0 0.244907 0 0.324154 0.376175 9999 66.6667
+9 0.0961391 0 0.292964 0 0.195655 0.415242 9999 75
+10 0.00327789 0.056797 0.592214 0 0.108561 0.23915 9999 83.3333
+11 0.0898729 0 0.220724 0 0.142796 0.546608 9999 91.6667
+12 0.11715 0 0.186571 0 0.171024 0.525256 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_fewshot3.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
+>44153 DEG expressed across 6 samples were identified
+>Group size: 481, Kappa: 12.8671053188237
+>Best kappa: 12.8671053188237 
+>SVD UpperRightDiag: 60342
+>SVD LowerRightDiag: 4689.64
+>=============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 0.0291666 0.382535 0 0.219005 0.369293 9999 9.09091
+2 0.071216 0.00703171 0.448271 0.0485397 0.240293 0.184649 9999 18.1818
+3 0.113274 0 0.180008 0.147048 0.0763939 0.483276 9999 27.2727
+4 0.116071 0 0.162946 0.09386 0.143466 0.483656 9999 36.3636
+5 0.0548955 0.0197915 0.255246 0.0361238 0.142322 0.491622 9999 45.4545
+6 0.135094 0.026716 0.301306 0.0431026 0.227993 0.265789 9999 54.5455
+7 0.0179547 0.0244397 0.218918 0.0177332 0.295549 0.425405 9999 63.6364
+8 0.0329373 0.0377795 0.253217 0 0.206061 0.470005 9999 72.7273
+9 0 0 0.69544 0 0.0956875 0.208873 9999 81.8182
+10 0.0645813 0.0117557 0.188951 0 0.119508 0.615204 9999 90.9091
+11 0.0914625 0.00900582 0.164691 0 0.113844 0.620996 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_fewshot4.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
+>45593 DEG expressed across 6 samples were identified
+>Group size: 474, Kappa: 10.484106886885
+>Best kappa: 10.484106886885 
+>SVD UpperRightDiag: 60128.4
+>SVD LowerRightDiag: 5735.19
+>=============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 0.60398 0.0748945 0.101548 0.219577 9999 10
+2 0.0160469 0.0734395 0.303738 0.116683 0.264135 0.225958 9999 20
+3 0.0285168 0.107624 0.603812 0.10871 0.0296611 0.121677 9999 30
+4 0.0462915 0.0769986 0.102295 0.191577 0.211655 0.371183 9999 40
+5 0.0441096 0.0400439 0.175352 0.185688 0.205578 0.349229 9999 50
+6 0.0131109 0.0513124 0.055267 0 0.109691 0.770618 9999 60
+7 0.0766422 0.0239907 0.140404 0.00048782 0.0521194 0.706356 9999 70
+8 0.0368341 0.036752 0.192858 0 0.231585 0.50197 9999 80
+9 0.0373293 0.0213613 0.114916 0.0400504 0.2151 0.571243 9999 90
+10 0.0411904 0.0359353 0.198823 0.0309644 0.1713 0.521787 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_immicro_cv0.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 16131 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>49579 DEG expressed across 6 samples were identified
+>Group size: 481, Kappa: 13.3264362095428
+>Best kappa: 13.3264362095428 
+>SVD UpperRightDiag: 39341.3
+>SVD LowerRightDiag: 2952.12
+>=============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 0.0193576 0.0828028 0.186066 0 0.20584 0.505934 9999 4.54545
+2 0.0707616 0.250757 0.191547 0.0230673 0.262359 0.201509 9999 9.09091
+3 0.0414983 0.0237967 0.185377 0 0.199316 0.550012 9999 13.6364
+4 0.0627245 0.0628919 0.294477 0 0.274924 0.304982 9999 18.1818
+5 0.0340706 0.0219887 0.265838 0 0.155327 0.522776 9999 22.7273
+6 0.0302673 0.0792218 0.197761 0.0154938 0.379975 0.297282 9999 27.2727
+7 0.0743289 0 0.27374 0 0.294896 0.357036 9999 31.8182
+8 0.112837 0.0407631 0.310715 0.00125361 0.262788 0.271643 9999 36.3636
+9 0.104152 0 0.37423 0.0406927 0.287236 0.193688 9999 40.9091
+10 0.101107 0.012763 0.154662 0.0326516 0.214789 0.484028 9999 45.4545
+11 0.0310051 0.119016 0.232699 0.133448 0.116559 0.367273 9999 50
+12 0.0560912 0.0515573 0.23432 0.104417 0.259785 0.29383 9999 54.5455
+13 0.0869496 0.00961417 0.292007 0 0.264944 0.346486 9999 59.0909
+14 0.0177001 0.106445 0.164933 0 0.191964 0.518959 9999 63.6364
+15 0.0980201 0.0294845 0.1362 0 0.361403 0.374892 9999 68.1818
+16 0.0831007 0.0347182 0.285344 0 0.246256 0.350581 9999 72.7273
+17 0.110912 0 0.384351 0 0.238518 0.266219 9999 77.2727
+18 0.0913958 0.157855 0.239295 0.0941312 0.078723 0.3386 9999 81.8182
+19 0.151644 0.069961 0.122669 0 0.230339 0.425387 9999 86.3636
+20 0.0704759 0.0645322 0.410551 0.0194426 0.242922 0.192076 9999 90.9091
+21 0.0202872 0.0371949 0.295102 0.0844899 0.21001 0.352916 9999 95.4545
+22 0.0731741 0.0343772 0.134623 0 0.1918 0.566026 9999 100