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/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 25 mixture samples, 5927 genes, and 6 cell subsets...
+>Window size adaptively set to 13
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 373

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 19656 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51155 DEG expressed across 6 samples were identified
+>Group size: 499, Kappa: 32.5850504252505
+>Best kappa: 32.5850504252505 
+>SVD UpperRightDiag: 153248
+>SVD LowerRightDiag: 4703
+>=============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 0.0829766 0.260368 0.166036 0.0544883 0.0659492 0.370182 9999 4
+2 0.0896435 0 0.268298 0 0.0198014 0.622257 9999 8
+3 0.10466 0.0073057 0.214039 0 0.028513 0.645482 9999 12
+4 0.143654 0.0526689 0.244947 0 0.00629355 0.552437 9999 16
+5 0.0619039 0.269267 0.167777 0.154345 0.061158 0.28555 9999 20
+6 1.697e-05 0.120334 0.23588 0.0736726 0.0310427 0.539054 9999 24
+7 0.0689578 0 0.316203 0.213319 0.270941 0.130579 9999 28
+8 0.0227861 0 0.434584 0.133051 0.3633 0.0462784 9999 32
+9 0.0519516 0 0.60956 0.0596415 0.140771 0.138076 9999 36
+10 0.00790216 0 0.384362 0.127581 0.144986 0.335169 9999 40
+11 0.0490276 0.118732 0.210249 0.215645 0.0587872 0.34756 9999 44
+12 0.0513939 0.107819 0.205465 0.202695 0.0353286 0.397298 9999 48
+13 0 0.297988 0.276952 0.112676 0.0254141 0.28697 9999 52
+14 0.00187489 0.0725744 0.456403 0.166074 0.129411 0.173663 9999 56
+15 0.0372417 0 0.770698 0.0633159 0.0880507 0.040694 9999 60
+16 0.0866766 0.170799 0.476142 0.0585989 0.0858063 0.121977 9999 64
+17 0.054615 0.0645006 0.597611 0.0165661 0.128166 0.138542 9999 68
+18 0.00275446 0.0328704 0.552275 0.0553721 0.226416 0.130312 9999 72
+19 0 0.022267 0.45405 0.0331692 0.384792 0.105721 9999 76
+20 0.0456287 0.0803551 0.468202 0.0239615 0.155859 0.225994 9999 80
+21 0 0.110707 0.375579 0.0297919 0.105605 0.378317 9999 84
+22 0.0352834 0.0796006 0.0290278 0.238281 0.00508879 0.612718 9999 88
+23 0.00848864 0.108109 0.289122 0 0.0468136 0.547467 9999 92
+24 0.0568008 0.140468 0.237512 0.0491349 0.0237363 0.492349 9999 96
+25 0.124022 0.172855 0.116613 0 0.02509 0.561419 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 29 mixture samples, 5927 genes, and 6 cell subsets...
+>Window size adaptively set to 15
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 407

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 19656 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>51506 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 39.500994128976
+>Best kappa: 39.500994128976 
+>SVD UpperRightDiag: 186232
+>SVD LowerRightDiag: 4714.62
+>=============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 0.122401 0.0417029 0.13187 0 0.034833 0.669193 9999 3.44828
+2 0.0397972 0.108773 0.263767 0 0.0561238 0.531539 9999 6.89655
+3 0.039245 0.0959353 0.206347 0 0.062293 0.59618 9999 10.3448
+4 0 0 0.472864 0.350509 0.0744587 0.102169 9999 13.7931
+5 0 0 0.507717 0.393959 0.0629001 0.0354245 9999 17.2414
+6 0 0 0.446749 0.394969 0.106796 0.0514857 9999 20.6897
+7 0.100278 0.107815 0.249679 0.148044 0.0941062 0.300078 9999 24.1379
+8 0.0686545 0 0.460026 0.122383 0.188654 0.160282 9999 27.5862
+9 0.0667807 0.000699931 0.370119 0.155153 0.237165 0.170083 9999 31.0345
+10 0.0382855 0.0282379 0.320739 0.11959 0.165707 0.327441 9999 34.4828
+11 0.0519972 0.0282781 0.388903 0.124541 0.0189359 0.387345 9999 37.931
+12 0.0485116 0 0.426222 0.138472 0.0185177 0.368276 9999 41.3793
+13 0.0198861 0.146983 0.272214 0.0509507 0.00513136 0.504835 9999 44.8276
+14 0.0865482 0.0785638 0.372506 0.0494263 0.0141849 0.398771 9999 48.2759
+15 0.102549 0.0706767 0.401198 0.0365155 0.126011 0.26305 9999 51.7241
+16 0.338487 0.019884 0.147486 0 0.0274681 0.466675 9999 55.1724
+17 0.173443 0.075191 0.484233 0.0602467 0.0282564 0.17863 9999 58.6207
+18 0.290884 0.0419179 0.337512 0.117429 0.0428163 0.169441 9999 62.069
+19 0.268785 0.022502 0.210483 0.0528694 0.0212468 0.424114 9999 65.5172
+20 0.213406 0 0.124926 0.0412397 0.0543711 0.566056 9999 68.9655
+21 0.22791 0.0879219 0.294619 0.0432817 0.0278771 0.31839 9999 72.4138
+22 0.212857 0.0680774 0.249339 0.0257315 0.0201894 0.423806 9999 75.8621
+23 0.236751 0.0466351 0.23567 0.00898268 0.0455597 0.426402 9999 79.3103
+24 0.105799 0.0906629 0.259006 0.0415166 0.0576764 0.445339 9999 82.7586
+25 0.034642 0.000975223 0.539902 0.154295 0.121901 0.148284 9999 86.2069
+26 0.0335531 0.0651192 0.392241 0.0829083 0.140063 0.286116 9999 89.6552
+27 0.0435676 0.0177806 0.158629 0.221848 0.0257338 0.532441 9999 93.1034
+28 0.0016129 0.153098 0.353164 0.0270112 0.0587101 0.406404 9999 96.5517
+29 0.0179606 0.0523485 0.196238 0.0502295 0.0246424 0.658581 9999 100