Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot4/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 19167 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>49221 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 8.8817857102621
+>Best kappa: 8.8817857102621 
+>SVD UpperRightDiag: 37004.9
+>SVD LowerRightDiag: 4166.38
+>=============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 0.176062 0.170818 0.139661 0.00236117 0.130489 0.380608 9999 4.16667
+2 0.0842802 0.0614801 0.194191 0.0780196 0.260065 0.321964 9999 8.33333
+3 0.0942613 0.0413219 0.260914 0.0860985 0.278976 0.238428 9999 12.5
+4 0.184296 0.0446817 0.308976 0.0952053 0.296916 0.0699254 9999 16.6667
+5 0.103663 0 0.455219 0.0404345 0.246482 0.154202 9999 20.8333
+6 0.155489 0 0.537717 0.00514263 0.0839948 0.217657 9999 25
+7 0.135944 0.0561472 0.355953 0.0227686 0.391988 0.0371996 9999 29.1667
+8 0.100634 0.183155 0.382719 0.0306772 0.29724 0.00557466 9999 33.3333
+9 0.126729 0.14137 0.343626 0 0.0991616 0.289113 9999 37.5
+10 0.0928593 0.209889 0.301599 0.00489504 0.104077 0.28668 9999 41.6667
+11 0.0294836 0 0.553729 0.0238771 0.115038 0.277872 9999 45.8333
+12 0.0267615 0.100653 0.141391 0.033068 0.332455 0.365672 9999 50
+13 0.03077 0.0189953 0.246229 0 0.0569662 0.647039 9999 54.1667
+14 0.0233388 0.215366 0.127907 0.0191219 0.194598 0.419668 9999 58.3333
+15 0.071468 0.0930764 0.287726 0.0587813 0.17021 0.318738 9999 62.5
+16 0.120373 0.0142216 0.388187 0.0420431 0.160816 0.274359 9999 66.6667
+17 0.212815 0.0546567 0.4604 0.0324716 0.108129 0.131527 9999 70.8333
+18 0.130151 0.222732 0.13054 0.0287978 0.129989 0.357789 9999 75
+19 0.0809963 0.166357 0.100663 0.0344504 0.185143 0.43239 9999 79.1667
+20 0.0390075 0 0.348979 0.0798346 0.214113 0.318066 9999 83.3333
+21 0.0182285 0.0644923 0.147334 0.165445 0.12385 0.480649 9999 87.5
+22 0.0741464 0.080281 0.238307 0.0976696 0.301975 0.207621 9999 91.6667
+23 0.112182 0.1315 0.199474 0.0934478 0.24933 0.214066 9999 95.8333
+24 0.0843584 0 0.469674 0.0842056 0.191251 0.170512 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv0/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 17 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 9
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 278

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv0/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
+>52028 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 28.748669174394
+>Best kappa: 28.748669174394 
+>SVD UpperRightDiag: 110560
+>SVD LowerRightDiag: 3845.76
+>=============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 0.0772717 0.259628 0.0992794 0.0681464 0.0738841 0.42179 9999 5.88235
+2 0.272459 0 0.109503 0 0.298801 0.319237 9999 11.7647
+3 0 0.329654 0.192528 0.0987969 0.235142 0.143879 9999 17.6471
+4 0.0263172 0.149729 0.339081 0.088618 0.259725 0.13653 9999 23.5294
+5 0.199974 0.0289728 0.0205444 0 0.00350011 0.747009 9999 29.4118
+6 0.0656272 0.16731 0.362536 0.190348 0.0727695 0.14141 9999 35.2941
+7 0.0164348 0.398169 0 0.0937174 0.0100321 0.481647 9999 41.1765
+8 0 0.401328 0 0.336935 0.0132156 0.248521 9999 47.0588
+9 0.0838898 0.221521 0.126188 0 0.0875944 0.480807 9999 52.9412
+10 0.20453 0.0933973 0 0.0105491 0 0.691523 9999 58.8235
+11 0.0102802 0.268455 0.262322 0 0.0273264 0.431617 9999 64.7059
+12 0.413874 0.0165607 0.0531148 0 0.00104751 0.515403 9999 70.5882
+13 0 0.229483 0.244836 0.334555 0.00282725 0.188299 9999 76.4706
+14 0.0819009 0.0533682 0.197613 0.111221 0.103897 0.452 9999 82.3529
+15 0.0400236 0.146649 0.271498 0 0.144038 0.397792 9999 88.2353
+16 0.157151 0.0755886 0.260556 0.0391869 0.213026 0.254491 9999 94.1176
+17 0.138035 0.167303 0.0466769 0.0067753 0.0231733 0.618036 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/cv1/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 17 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 9
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 325