Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv1/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 19864 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>52778 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 28.5479259649129
+>Best kappa: 28.5479259649129 
+>SVD UpperRightDiag: 113755
+>SVD LowerRightDiag: 3984.69
+>=============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 0.0256801 0.0870406 0.0175124 0.271429 0.0110252 0.587313 9999 5.88235
+2 0.0865785 0.199834 0.316034 0.076733 0.0444153 0.276405 9999 11.7647
+3 0.0123629 0.295246 0.315556 0.0520229 0.131562 0.19325 9999 17.6471
+4 0.0870477 0.166716 0 0.235042 0 0.511195 9999 23.5294
+5 0.0815971 0.182672 0 0.243161 0.00738415 0.485186 9999 29.4118
+6 0.182292 0.126493 0.34983 0.120963 0.0659272 0.154495 9999 35.2941
+7 0.203704 0.139773 0.0178761 0.0878434 0.0160956 0.534708 9999 41.1765
+8 0.229989 0.19976 0.081445 0 0.0107534 0.478052 9999 47.0588
+9 0.380963 0 0.206292 0 0.0381655 0.37458 9999 52.9412
+10 0.0168165 0.283798 0.210014 0.0414026 0.00016732 0.447802 9999 58.8235
+11 0.022671 0.00704047 0.0639554 0 0.180791 0.725542 9999 64.7059
+12 0.0579999 0.0590988 0.275497 0.202598 0.037619 0.367187 9999 70.5882
+13 0.0322009 0.119037 0.127708 0.163831 0.183315 0.373908 9999 76.4706
+14 0.0314842 0.250125 0.39147 0.0446532 0.0190592 0.263209 9999 82.3529
+15 0.0453576 0.175666 0.238931 0.0923008 0.199414 0.248331 9999 88.2353
+16 0.172002 0 0.062299 0 0.250582 0.515117 9999 94.1176
+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/cibersortx/ye2026_sepsis/cv2/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 16 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 8
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 301

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv2/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 19864 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>52065 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 33.1777193154457
+>Best kappa: 33.1777193154457 
+>SVD UpperRightDiag: 126436
+>SVD LowerRightDiag: 3810.86
+>=============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 0.0769123 0.246751 0.492016 0.0165502 0.116914 0.0508554 9999 6.25
+2 0.361201 0.0356112 0.138966 0.0337737 0.254753 0.175696 9999 12.5
+3 0 0.298148 0.142137 0.0689792 0.102715 0.388022 9999 18.75
+4 0.175458 0.0587669 0.380163 0.0251828 0.0383912 0.322038 9999 25
+5 0.0276362 0.255214 0 0.210045 0 0.507105 9999 31.25
+6 0.121946 0.0871905 0.0676515 0.130892 0.105387 0.486933 9999 37.5
+7 0.0438018 0.368026 0.171199 0 0.116207 0.300766 9999 43.75
+8 0.0763387 0.290908 0 0.0351648 0.0169139 0.580675 9999 50
+9 0.197907 0 0.0798405 0 0 0.722252 9999 56.25
+10 0.111448 0.101647 0.28727 0 0.0239852 0.47565 9999 62.5
+11 0.141834 0.160343 0.338337 0.120098 0.208568 0.0308192 9999 68.75
+12 0.0856207 0.168768 0.055186 0.0352768 0.0979996 0.557149 9999 75
+13 0.294967 0.0490707 0.0455418 0.0866765 0 0.523744 9999 81.25
+14 0.118653 0.162697 0.14224 0.0484612 0.0646966 0.463252 9999 87.5
+15 0 0.349098 0.140414 0.0767698 0.00742236 0.426296 9999 93.75
+16 0.00978047 0.0235317 0.00538733 0.279581 0.00565527 0.676064 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv3/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 16 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 8
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 292