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/fewshot0/out_fractions/.run.log

@@ -0,0 +1,74 @@
+>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
+>50042 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 10.5746849842615
+>Best kappa: 10.5746849842615 
+>SVD UpperRightDiag: 44059.5
+>SVD LowerRightDiag: 4166.51
+>=============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 0.0738397 0.0886976 0.22552 0.0802023 0.0654695 0.466271 9999 4
+2 0.106747 0 0.233231 0.158156 0.185651 0.316215 9999 8
+3 0.111482 0.0514896 0.167551 0.0925758 0.362518 0.214384 9999 12
+4 0.119566 0.00512937 0.199177 0.105644 0.433408 0.137075 9999 16
+5 0.19237 0 0.275091 0.0750028 0.432891 0.0246457 9999 20
+6 0.128345 0 0.283832 0.0496679 0.538155 0 9999 24
+7 0.11481 0 0.372639 0.0221537 0.381568 0.108829 9999 28
+8 0.141051 0.108033 0.269498 0.0133891 0.311589 0.156439 9999 32
+9 0.109311 0.161762 0.230043 0.0437507 0.267194 0.18794 9999 36
+10 0.129215 0.0928495 0.221824 0.0354936 0.320504 0.200114 9999 40
+11 0.0921064 0.0967464 0.185251 0.0661411 0.367295 0.19246 9999 44
+12 0.0714754 0 0.328784 0.0387066 0.493121 0.0679129 9999 48
+13 0.0812223 0.0676638 0.136644 0.0241137 0.656176 0.0341807 9999 52
+14 0.0975355 0 0.133734 0.0159683 0.425421 0.327342 9999 56
+15 0.1021 0.114719 0.0707357 0.0470806 0.519682 0.145683 9999 60
+16 0.107345 0.0335314 0.147476 0.0573348 0.612267 0.0420458 9999 64
+17 0.151652 0.134773 0.138305 0.0391262 0.297004 0.23914 9999 68
+18 0.0915965 0.17776 0.0732726 0.0454914 0.506444 0.105435 9999 72
+19 0.0967829 0.0170718 0.163514 0.0625758 0.623193 0.036862 9999 76
+20 0.053853 0.075548 0.0781094 0.21504 0.232522 0.344927 9999 80
+21 0.0996612 0 0.297348 0.101137 0.333629 0.168224 9999 84
+22 0.0824533 0.0112781 0.118504 0.199008 0.341838 0.246919 9999 88
+23 0.0910215 0.0196851 0.102474 0.0874215 0.699397 0 9999 92
+24 0.108752 0.0230549 0.104637 0.094441 0.669115 0 9999 96
+25 0.118454 0 0.388123 0.090086 0.337077 0.0662594 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot1/hires_run.log

@@ -0,0 +1,15 @@
+>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 26 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): 283

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot1/out_fractions/.run.log

@@ -0,0 +1,75 @@
+>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
+>52983 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 21.2987056514988
+>Best kappa: 21.2987056514988 
+>SVD UpperRightDiag: 92685.3
+>SVD LowerRightDiag: 4351.69
+>=============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 0.0784339 0.058582 0.238997 0.146281 0.0217097 0.455997 9999 3.84615
+2 0.0837314 0 0.270095 0.212482 0.0938912 0.339801 9999 7.69231
+3 0.151619 0.120252 0.0938678 0.0549612 0.260665 0.318635 9999 11.5385
+4 0.100097 0.0346299 0.199632 0.162769 0.203836 0.299036 9999 15.3846
+5 0.107498 0.00443301 0.240804 0.183253 0.250302 0.21371 9999 19.2308
+6 0.231304 0.0330638 0.24968 0.119526 0.264009 0.102418 9999 23.0769
+7 0.126081 0 0.291094 0.0717664 0.481002 0.0300568 9999 26.9231
+8 0.095802 0.135087 0.239216 0.0719812 0.441951 0.0159618 9999 30.7692
+9 0.103716 0.183665 0.209819 0.0586143 0.191371 0.252815 9999 34.6154
+10 0.0677172 0.158411 0.177486 0.12242 0.228681 0.245284 9999 38.4615
+11 0.0456367 0.00339396 0.410458 0.059573 0.320725 0.160213 9999 42.3077
+12 0.0709984 0.159778 0.145597 0.0344337 0.415435 0.173758 9999 46.1538
+13 0.0972149 0.0993773 0.128949 0.0758066 0.343003 0.25565 9999 50
+14 0.175863 0.00349073 0.181502 0.118145 0.392616 0.128383 9999 53.8462
+15 0.124244 0.149925 0.17823 0.0431846 0.196072 0.308344 9999 57.6923
+16 0.0672394 0.207857 0.130138 0.0764784 0.331924 0.186364 9999 61.5385
+17 0.0588549 0.119212 0.164437 0.11043 0.406489 0.140577 9999 65.3846
+18 0.00730232 0.0943892 0.102705 0.220636 0.128716 0.446252 9999 69.2308
+19 0.189223 0 0.273944 0.10302 0.279813 0.154 9999 73.0769
+20 0.213251 0 0.345082 0.130607 0.212567 0.0984925 9999 76.9231
+21 0.202847 0.0524907 0.151359 0.100432 0.2344 0.258472 9999 80.7692
+22 0.033459 0.117432 0.0439954 0.0566701 0.488122 0.260322 9999 84.6154
+23 0.0980948 0 0.29762 0.194888 0.197685 0.211713 9999 88.4615
+24 0.0803369 0.0415101 0.100034 0.284214 0.211492 0.282414 9999 92.3077
+25 0.127005 0.0385367 0.126155 0.143991 0.478873 0.0854395 9999 96.1538
+26 0.100902 0 0.432362 0.129406 0.210492 0.126838 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/fewshot2/hires_run.log

@@ -0,0 +1,15 @@
+>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 26 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): 255