Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 24 mixture samples, 5927 genes, and 6 cell subsets...
+>Window size adaptively set to 12
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 360

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 19656 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51709 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 19.2614679694143
+>Best kappa: 19.2614679694143 
+>SVD UpperRightDiag: 95591.2
+>SVD LowerRightDiag: 4962.82
+>=============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 0.0596931 0 0.287139 0.0269527 0.040376 0.585839 9999 4.16667
+2 0.00291327 0.0641649 0.452369 0.0284206 0.0500177 0.402115 9999 8.33333
+3 0 0.0594086 0.489078 0.0247644 0.0909554 0.335793 9999 12.5
+4 0.109271 0 0.64679 0 0.0634497 0.18049 9999 16.6667
+5 0.123364 0.0718531 0.296221 0.0185938 0.0688581 0.42111 9999 20.8333
+6 0.113824 0.0464674 0.256785 0 0.070852 0.512071 9999 25
+7 0.10023 0.169655 0.206982 0.0751058 0.0650586 0.382969 9999 29.1667
+8 0.165693 0.0184752 0.176891 0.0689377 0.00729391 0.562709 9999 33.3333
+9 0.113371 0.0745297 0.209921 0.111877 0.0232779 0.467024 9999 37.5
+10 0.211931 0 0.162018 0 0.0178061 0.608245 9999 41.6667
+11 0.0259865 0.150276 0.181278 0.0918685 0.0136194 0.536972 9999 45.8333
+12 0.153042 0.123429 0.302642 0.0915186 0.0122213 0.317147 9999 50
+13 0.164817 0.0911944 0.357797 0.0827876 0.0609356 0.242468 9999 54.1667
+14 0.131825 0.0575003 0.374257 0.18144 0.0272817 0.227695 9999 58.3333
+15 0.119394 0.0272299 0.515489 0.0824454 0.0505549 0.204887 9999 62.5
+16 0.153193 0.0494343 0.385051 0.0557335 0.0539642 0.302623 9999 66.6667
+17 0.156342 0.0641661 0.372693 0.12873 0.0698895 0.20818 9999 70.8333
+18 0.0141807 0.121905 0.212804 0.177001 0.00641263 0.467697 9999 75
+19 0.0347947 0.043347 0.28835 0.262901 0.0222503 0.348357 9999 79.1667
+20 0.105588 0.0346221 0.169637 0.184228 0.0578604 0.448064 9999 83.3333
+21 0.0837773 0.0559285 0.143022 0.213053 0.0774628 0.426756 9999 87.5
+22 0.0505307 0.0646274 0.143362 0.221983 0.0609277 0.45857 9999 91.6667
+23 0.038936 0.144544 0.147253 0.234631 0.0259596 0.408677 9999 95.8333
+24 0.128084 0.0206225 0.379578 0.121547 0.0672649 0.282903 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 32 mixture samples, 5927 genes, and 6 cell subsets...
+>Window size adaptively set to 16
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 448

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 19656 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51807 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 41.3214745511455
+>Best kappa: 41.3214745511455 
+>SVD UpperRightDiag: 183830
+>SVD LowerRightDiag: 4448.78
+>=============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 0.186703 0.0205915 0.554608 0.0711086 0.0348492 0.13214 9999 3.125
+2 0.172456 0 0.463489 0.203751 0.0292121 0.131092 9999 6.25
+3 0 0.068876 0.353809 0 0.0377036 0.539612 9999 9.375
+4 0.054243 0.0559838 0.250096 0 0.0527918 0.586885 9999 12.5
+5 0.039177 0.127 0.241335 0 0.0444404 0.548047 9999 15.625
+6 0.102385 0.0475313 0.385701 0.0393323 0.0518071 0.373244 9999 18.75
+7 0.0238128 0.047207 0.29277 0.0948577 0.0856432 0.455709 9999 21.875
+8 0.083911 0.0251154 0.476202 0.0290383 0.0717321 0.314001 9999 25
+9 0 0.0703015 0.341439 0.180513 0.0493753 0.358372 9999 28.125
+10 0.00153304 0.039193 0.508811 0.0486623 0.0904993 0.311302 9999 31.25
+11 0 0.106728 0.325218 0.0426805 0.138002 0.387371 9999 34.375
+12 0 0.152816 0.259885 0.0371098 0.0599697 0.490219 9999 37.5
+13 0 0.109308 0.249767 0.109745 0.0652133 0.465967 9999 40.625
+14 0.00604224 0.14566 0.310188 0.0402951 0.0442742 0.453541 9999 43.75
+15 0.0240608 0 0.415647 0 0.0399643 0.520328 9999 46.875
+16 0.0133077 0.145284 0.474953 0.130162 0.00606215 0.230231 9999 50
+17 0 0.144806 0.365374 0.151478 0.0807152 0.257627 9999 53.125
+18 0 0.168054 0.280606 0.129551 0.0400772 0.381713 9999 56.25
+19 0.0885957 0.134061 0.151038 0.169921 0.0160473 0.440337 9999 59.375
+20 0.0175484 0.13876 0.24821 0.114501 0.0956692 0.385312 9999 62.5
+21 0.0582598 0.0493555 0.265959 0.0923441 0.0358668 0.498215 9999 65.625
+22 0.0622815 0.0429291 0.206966 0.280106 0.0434805 0.364237 9999 68.75
+23 0.0684202 0.0872129 0.148378 0.175844 0.0867133 0.433432 9999 71.875
+24 0.0532529 0.0621759 0.112083 0.142014 0.176184 0.454291 9999 75
+25 0.0255135 0.0364141 0.378043 0.172834 0.0787917 0.308403 9999 78.125
+26 0.0276726 0 0.618487 0.173884 0.0484157 0.131541 9999 81.25
+27 0.0237547 0 0.625974 0.159523 0.0557731 0.134975 9999 84.375
+28 0.0559105 0.0270582 0.546256 0.151714 0.120714 0.0983468 9999 87.5
+29 0.039764 0.00688662 0.497947 0.148712 0.110094 0.196597 9999 90.625
+30 0.0217801 0.104038 0.358028 0.0630134 0.125548 0.327592 9999 93.75
+31 0.0408129 0.11175 0.21866 0 0.0599003 0.568876 9999 96.875
+32 0.00937267 0.126506 0.257184 0.068301 0.0465982 0.492038 9999 100