Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot1/hires_run.log

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+>Running CIBERSORTx high-resolution GEP imputation...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] mixture: mixture.txt
+>[Options] sigmatrix: sigmatrix.txt
+>[Options] cibresults: fractions_results.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] sourceGEPs: source_geps.txt
+>[Options] subsetgenes: hires_genes.txt
+>[Options] threads: 4
+>Loaded 10 mixture samples, 5563 genes, and 6 cell subsets...
+>Window size adaptively set to 7
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 108

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot1/out_fractions/.run.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

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot2/hires_run.log

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+>Running CIBERSORTx high-resolution GEP imputation...
+>[Options] username: [REDACTED]
+>[Options] token: [REDACTED]
+>[Options] mixture: mixture.txt
+>[Options] sigmatrix: sigmatrix.txt
+>[Options] cibresults: fractions_results.txt
+>[Options] rmbatchSmode: TRUE
+>[Options] sourceGEPs: source_geps.txt
+>[Options] subsetgenes: hires_genes.txt
+>[Options] threads: 4
+>Loaded 12 mixture samples, 5563 genes, and 6 cell subsets...
+>Window size adaptively set to 7
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 147

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot2/out_fractions/.run.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