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/fewshot2/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
+>48524 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 21.6210558153982
+>Best kappa: 21.6210558153982 
+>SVD UpperRightDiag: 90279.7
+>SVD LowerRightDiag: 4175.54
+>=============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 0.125973 0.0234502 0.290469 0.0292703 0.0401104 0.490727 9999 3.84615
+2 0.0913118 0 0.281375 0.118341 0.122947 0.386025 9999 7.69231
+3 0.0789818 0.0170442 0.224553 0.128357 0.25199 0.299074 9999 11.5385
+4 0.0914888 0.0169122 0.256913 0.118312 0.300366 0.216008 9999 15.3846
+5 0.206496 0.0114749 0.307039 0.103392 0.313226 0.0583727 9999 19.2308
+6 0.0831949 0 0.411322 0.0186619 0.486821 0 9999 23.0769
+7 0.129517 0 0.495349 0.000249277 0.282705 0.0921795 9999 26.9231
+8 0.0651328 0.0295455 0.266015 0.0487119 0.590595 0 9999 30.7692
+9 0.0359184 0.124906 0.264024 0.0338982 0.541254 0 9999 34.6154
+10 0.102639 0.114342 0.330039 0 0.216525 0.236455 9999 38.4615
+11 0.0699071 0.148655 0.321603 0 0.199521 0.260313 9999 42.3077
+12 0.0741891 0.11625 0.296863 0.00427723 0.251768 0.256653 9999 46.1538
+13 0.074068 0.102823 0.221024 0.0745983 0.267321 0.260166 9999 50
+14 0.0578304 0.0693949 0.185497 0.082924 0.259717 0.344636 9999 53.8462
+15 0.051962 0.11446 0.207248 0.00782474 0.552143 0.0663625 9999 57.6923
+16 0.0638401 0 0.191303 0 0.346251 0.398606 9999 61.5385
+17 0.0653172 0.108551 0.133894 0.0600642 0.405424 0.226751 9999 65.3846
+18 0.0872944 0.0644705 0.209673 0.0813705 0.515762 0.0414295 9999 69.2308
+19 0.129766 0.159542 0.190858 0.0162791 0.210469 0.293086 9999 73.0769
+20 0.108102 0.174088 0.153627 0.04215 0.382785 0.139248 9999 76.9231
+21 0.122825 0 0.321454 0.0346328 0.368019 0.153069 9999 80.7692
+22 0.227727 0 0.408058 0.0387911 0.259394 0.0660302 9999 84.6154
+23 0.056249 0 0.327767 0.0996866 0.270469 0.245828 9999 88.4615
+24 0.0460354 0.0400478 0.135076 0.185516 0.249105 0.344219 9999 92.3077
+25 0.127405 0.0624479 0.139303 0.109096 0.561748 0 9999 96.1538
+26 0.104237 0 0.454807 0.084185 0.248466 0.108305 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot3/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, 5752 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): 218

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot3/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
+>51788 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 27.6482103115097
+>Best kappa: 27.6482103115097 
+>SVD UpperRightDiag: 114191
+>SVD LowerRightDiag: 4130.14
+>=============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 0.0795596 0.109506 0.226209 0 0.0326814 0.552043 9999 4
+2 0.0777906 0 0.256628 0.109855 0.11224 0.443486 9999 8
+3 0.124301 0.148681 0.127253 0 0.254646 0.345119 9999 12
+4 0.172951 0.0296916 0.305751 0.0872367 0.282885 0.121484 9999 16
+5 0.083948 0 0.339405 0.0580704 0.45272 0.0658563 9999 20
+6 0.120407 0 0.43976 0.0107294 0.271336 0.157768 9999 24
+7 0.0986515 0.0348122 0.274293 0.0354802 0.527508 0.0292551 9999 28
+8 0.0869008 0.106667 0.273021 0.0335878 0.491729 0.00809487 9999 32
+9 0.107031 0.1388 0.276323 0 0.206867 0.27098 9999 36
+10 0.100713 0.226921 0.233241 0.00966693 0.16049 0.268968 9999 40
+11 0.1185 0.156494 0.2272 0.0281817 0.206883 0.262742 9999 44
+12 0.0804666 0.137716 0.190035 0.0898207 0.242913 0.259048 9999 48
+13 0.116841 0.0965026 0.166101 0.0202938 0.460376 0.139885 9999 52
+14 0.0787157 0.0220237 0.157183 0 0.318986 0.423092 9999 56
+15 0.0813075 0.217608 0.13976 0.0120187 0.193149 0.356157 9999 60
+16 0.0535455 0.235813 0.103431 0.0450104 0.351925 0.210276 9999 64
+17 0.0677373 0.0814652 0.183183 0.0649009 0.44048 0.162234 9999 68
+18 0.0273005 0.0830353 0.0886237 0.150885 0.132445 0.51771 9999 72
+19 0.151963 0 0.279453 0.0534927 0.329447 0.185645 9999 76
+20 0.215034 0 0.395311 0.0445822 0.237762 0.10731 9999 80
+21 0.0717992 0 0.314514 0.0916297 0.230982 0.291075 9999 84
+22 0.0631536 0.0280576 0.129644 0.160363 0.21079 0.407991 9999 88
+23 0.0514789 0.0616736 0.142212 0.0743795 0.51559 0.154666 9999 92
+24 0.0680261 0.0907977 0.121272 0.0961377 0.501474 0.122293 9999 96
+25 0.0805172 0 0.422702 0.064433 0.242523 0.189824 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot4/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, 5752 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): 240