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/cv3/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
+>51636 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 45.2108782760634
+>Best kappa: 45.2108782760634 
+>SVD UpperRightDiag: 163159
+>SVD LowerRightDiag: 3608.85
+>=============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 0.0840823 0.180414 0.371325 0.0144839 0.150683 0.199012 9999 6.25
+2 0.0801864 0.0265344 0.101973 0.0174009 0.331579 0.442326 9999 12.5
+3 0.246108 0.34273 0.146597 0.0594426 0.0261828 0.17894 9999 18.75
+4 0 0.176157 0.375323 0.0413307 0.407189 0 9999 25
+5 0.0624134 0.18442 0.0392742 0.282662 0 0.43123 9999 31.25
+6 0 0.324761 0.324425 0.0605526 0.0339116 0.256349 9999 37.5
+7 0.0969866 0.0770498 0.025564 0.0102329 0.0167539 0.773413 9999 43.75
+8 0.185872 0 0.0945884 0 0.129876 0.589664 9999 50
+9 0.264354 0 0.00450378 0 0.0781363 0.653005 9999 56.25
+10 0.150279 0.117906 0.17897 0.157173 0.0737532 0.321919 9999 62.5
+11 0.223462 0 0.162846 0.16086 0.0146133 0.438219 9999 68.75
+12 0 0.320075 0.321317 0 0 0.358608 9999 75
+13 0.0152062 0.324669 0.301484 0.102357 0.00949743 0.246786 9999 81.25
+14 0.123386 0.0225558 0.0947596 0.019839 0.00439194 0.735068 9999 87.5
+15 0 0.358389 0.223616 0.0547133 0.00109207 0.36219 9999 93.75
+16 0.056115 0.0851355 0.231879 0.00492056 0.146784 0.475166 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv4/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): 304

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv4/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
+>51640 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 24.8809089477405
+>Best kappa: 24.8809089477405 
+>SVD UpperRightDiag: 100871
+>SVD LowerRightDiag: 4054.17
+>=============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 0.600085 0 0.00107774 0 0 0.398837 9999 6.25
+2 0.0163531 0.0831437 0.0640051 0 0.0766331 0.759865 9999 12.5
+3 0.00393437 0.183244 0.140833 0.177412 0.0483912 0.446185 9999 18.75
+4 0.100394 0.160978 0.144393 0.326882 0.0590709 0.208282 9999 25
+5 0.00254274 0.199889 0.387005 0.158281 0.0991938 0.153089 9999 31.25
+6 0 0.178208 0 0.470726 0.000136932 0.350929 9999 37.5
+7 0.0113589 0.285988 0.0528768 0.132264 0 0.517513 9999 43.75
+8 0.277051 0.156789 0.00969477 0.0265443 0.0119741 0.517947 9999 50
+9 0.395036 0.121316 0.00173287 0.0186815 0.0141969 0.449037 9999 56.25
+10 0.25035 0.293954 0.202173 0 0.0275702 0.225953 9999 62.5
+11 0 0.395786 0.254976 0.0417213 0.0442673 0.263249 9999 68.75
+12 0.0985128 0.198802 0.0138332 0.107539 0.0126351 0.568678 9999 75
+13 0.192037 0.048722 0.339011 0.0385861 0.0197622 0.361881 9999 81.25
+14 0 0.353511 0.18463 0.145116 0.116985 0.199758 9999 87.5
+15 0 0.118086 0.0794082 0.0104561 0.238946 0.553104 9999 93.75
+16 0.126392 0.151135 0.113353 0.00823072 0.413704 0.187186 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot0/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 77 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 24
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 1102