Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv3.log

@@ -0,0 +1,65 @@
+>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
+>51636 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 45.2108782760634
+>Best kappa: 45.2108782760634 
+>SVD UpperRightDiag: 163159
+>SVD LowerRightDiag: 3608.85
+>=============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 0.0840823 0.180414 0.371325 0.0144839 0.150683 0.199012 9999 6.25
+2 0.0801864 0.0265344 0.101973 0.0174009 0.331579 0.442326 9999 12.5
+3 0.246108 0.34273 0.146597 0.0594426 0.0261828 0.17894 9999 18.75
+4 0 0.176157 0.375323 0.0413307 0.407189 0 9999 25
+5 0.0624134 0.18442 0.0392742 0.282662 0 0.43123 9999 31.25
+6 0 0.324761 0.324425 0.0605526 0.0339116 0.256349 9999 37.5
+7 0.0969866 0.0770498 0.025564 0.0102329 0.0167539 0.773413 9999 43.75
+8 0.185872 0 0.0945884 0 0.129876 0.589664 9999 50
+9 0.264354 0 0.00450378 0 0.0781363 0.653005 9999 56.25
+10 0.150279 0.117906 0.17897 0.157173 0.0737532 0.321919 9999 62.5
+11 0.223462 0 0.162846 0.16086 0.0146133 0.438219 9999 68.75
+12 0 0.320075 0.321317 0 0 0.358608 9999 75
+13 0.0152062 0.324669 0.301484 0.102357 0.00949743 0.246786 9999 81.25
+14 0.123386 0.0225558 0.0947596 0.019839 0.00439194 0.735068 9999 87.5
+15 0 0.358389 0.223616 0.0547133 0.00109207 0.36219 9999 93.75
+16 0.056115 0.0851355 0.231879 0.00492056 0.146784 0.475166 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_cv4.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
+>51640 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 24.8809089477405
+>Best kappa: 24.8809089477405 
+>SVD UpperRightDiag: 100871
+>SVD LowerRightDiag: 4054.17
+>=============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 0.600085 0 0.00107774 0 0 0.398837 9999 6.25
+2 0.0163531 0.0831437 0.0640051 0 0.0766331 0.759865 9999 12.5
+3 0.00393437 0.183244 0.140833 0.177412 0.0483912 0.446185 9999 18.75
+4 0.100394 0.160978 0.144393 0.326882 0.0590709 0.208282 9999 25
+5 0.00254274 0.199889 0.387005 0.158281 0.0991938 0.153089 9999 31.25
+6 0 0.178208 0 0.470726 0.000136932 0.350929 9999 37.5
+7 0.0113589 0.285988 0.0528768 0.132264 0 0.517513 9999 43.75
+8 0.277051 0.156789 0.00969477 0.0265443 0.0119741 0.517947 9999 50
+9 0.395036 0.121316 0.00173287 0.0186815 0.0141969 0.449037 9999 56.25
+10 0.25035 0.293954 0.202173 0 0.0275702 0.225953 9999 62.5
+11 0 0.395786 0.254976 0.0417213 0.0442673 0.263249 9999 68.75
+12 0.0985128 0.198802 0.0138332 0.107539 0.0126351 0.568678 9999 75
+13 0.192037 0.048722 0.339011 0.0385861 0.0197622 0.361881 9999 81.25
+14 0 0.353511 0.18463 0.145116 0.116985 0.199758 9999 87.5
+15 0 0.118086 0.0794082 0.0104561 0.238946 0.553104 9999 93.75
+16 0.126392 0.151135 0.113353 0.00823072 0.413704 0.187186 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_fewshot0.log

@@ -0,0 +1,126 @@
+>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
+>54042 DEG expressed across 6 samples were identified
+>Group size: 497, Kappa: 13.3470961575937
+>Best kappa: 13.3470961575937 
+>SVD UpperRightDiag: 55525.5
+>SVD LowerRightDiag: 4160.12
+>=============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 0.0371905 0.234849 0.600844 0.0445659 0.0557688 0.026782 9999 1.2987
+2 0.357834 0.059947 0.192693 0.0824832 0.161393 0.14565 9999 2.5974
+3 0 0.0929088 0.0164162 0.384638 0.0109618 0.495075 9999 3.8961
+4 0.114649 0.166212 0.233701 0.134086 0.0505181 0.300833 9999 5.19481
+5 0.677376 0 0 0 0 0.322624 9999 6.49351
+6 0.30716 0 0.16035 0 0.209284 0.323206 9999 7.79221
+7 0.0147384 0.0303953 0.0911672 0 0.0462598 0.817439 9999 9.09091
+8 0.0960536 0.165615 0.398781 0.0554548 0.170535 0.11356 9999 10.3896
+9 0.0482617 0.0517595 0.1723 0.030595 0.29064 0.406443 9999 11.6883
+10 0.0481324 0.207466 0.384373 0.132978 0.0246339 0.202416 9999 12.987
+11 0 0.272649 0.366091 0.178584 0.0892143 0.0934619 9999 14.2857
+12 0.0128619 0.266238 0.436969 0.0837246 0.0609284 0.139278 9999 15.5844
+13 0.0646911 0.100666 0.510222 0.111522 0.0951043 0.117794 9999 16.8831
+14 0.0470474 0.162065 0.204785 0.245715 0.0289464 0.31144 9999 18.1818
+15 0.262829 0.0169942 0.0148431 0 0.00290723 0.702427 9999 19.4805
+16 0.226398 0.287591 0.226301 0.0630541 0.0551368 0.141519 9999 20.7792
+17 0.141691 0.122384 0.174367 0.369076 0.039068 0.153414 9999 22.0779
+18 0 0.27886 0.219214 0.148004 0.0711903 0.282732 9999 23.3766
+19 0.1726 0.0351466 0.430801 0.0493269 0.0181779 0.293947 9999 24.6753
+20 0 0.282775 0.46488 0.0730781 0.179267 0 9999 25.974
+21 0 0.264804 0.432064 0.165687 0.0537523 0.0836926 9999 27.2727
+22 0.0346241 0.379755 0.0194315 0.151683 0.00999159 0.404515 9999 28.5714
+23 0.0923566 0.159292 0 0.360454 0 0.387896 9999 29.8701
+24 0.0299686 0.236384 0.00937304 0.332894 0 0.391381 9999 31.1688
+25 0.0206909 0.237539 0.00763951 0.405086 0.0107192 0.318326 9999 32.4675
+26 0.0912945 0.165318 0.00361959 0.388198 0.00720728 0.344363 9999 33.7662
+27 0.0038339 0.166185 0 0.624827 0.00440904 0.200745 9999 35.0649
+28 0.1377 0.0584467 0.105118 0.187524 0.0759247 0.435287 9999 36.3636
+29 0.0126738 0.220717 0.12958 0.244154 0.00170854 0.391167 9999 37.6623
+30 0.134656 0.113633 0.456247 0.152613 0.0315422 0.111309 9999 38.961
+31 0.058263 0.34084 0.246027 0.0464341 0.0701489 0.238286 9999 40.2597
+32 0 0.39551 0.339238 0.0730577 0.0378322 0.154362 9999 41.5584
+33 0.132064 0.1716 0.219585 0.0273561 0.0759259 0.373469 9999 42.8571
+34 0.21229 0.10814 0.0526612 0.184486 0.00976508 0.432658 9999 44.1558
+35 0.360215 0.0856698 0.0592125 0.0742231 0 0.42068 9999 45.4545
+36 0.243713 0.0958939 0 0.121173 0 0.53922 9999 46.7532
+37 0.0930325 0.233113 0.026118 0.122738 0.0132615 0.511737 9999 48.0519
+38 0.0903968 0.0241944 0.0879935 0.0744277 0.0265307 0.696457 9999 49.3506
+39 0.497639 0.0731412 0.0181735 0.0451439 0.0057118 0.360191 9999 50.6494
+40 0.0679163 0.196158 0.416805 0.00401293 0.00691136 0.308197 9999 51.9481
+41 0.253956 0.210045 0.120328 0 0.00954743 0.406124 9999 53.2468
+42 0.188066 0 0.158787 0.0758074 0.0261076 0.551232 9999 54.5455
+43 0.35581 0.17471 0.310097 0 0.0143859 0.144997 9999 55.8442
+44 0.340416 0 0.302531 0 0.00918347 0.34787 9999 57.1429
+45 0.312466 0.00690332 0 0 0.011835 0.668795 9999 58.4416
+46 0.0663731 0.139806 0.247277 0.205427 0.0956506 0.245465 9999 59.7403
+47 0.0302461 0.201288 0.315272 0.109209 0 0.343985 9999 61.039
+48 0.479666 0.0147027 0.0685951 0 0 0.437036 9999 62.3377
+49 0.233897 0 0.0986902 0 0 0.667412 9999 63.6364
+50 0.0112037 0.0010895 0.0792181 0 0.16262 0.745869 9999 64.9351
+51 0.16381 0.0242872 0.232533 0.20687 0 0.372499 9999 66.2338
+52 0.00506273 0.376986 0.324768 0.0577692 0.0289187 0.206496 9999 67.5325
+53 0 0.380892 0.339894 0 0.00322132 0.275993 9999 68.8312
+54 0 0.116896 0.39325 0.381865 0 0.107989 9999 70.1299
+55 0.0681285 0.120678 0.310546 0.0478831 0.0157256 0.437039 9999 71.4286
+56 0.0459223 0.207651 0.396653 0.128953 0.00876054 0.212061 9999 72.7273
+57 0.137223 0.186743 0.0253693 0.187322 0.0137571 0.449585 9999 74.026
+58 0.243253 0.0350475 0.367436 0.0509839 0.00147791 0.301802 9999 75.3247
+59 0.0965273 0.151059 0.0917451 0.0808216 0.0825733 0.497274 9999 76.6234
+60 0.262436 0.0371262 0.0716771 0.133907 0 0.494853 9999 77.9221
+61 0.0572402 0.0333051 0.352391 0.266578 0.0255108 0.264974 9999 79.2208
+62 0.0317047 0.054538 0.192795 0.250851 0.154604 0.315508 9999 80.5195
+63 0.0611506 0.0376773 0.306161 0.164699 0.0733968 0.356914 9999 81.8182
+64 0.132718 0.119129 0.208333 0.131053 0.047106 0.361661 9999 83.1169
+65 0 0.296274 0.246069 0.233716 0.094599 0.129342 9999 84.4156
+66 0.189137 0.0929294 0.386657 0.0696398 0.0818318 0.179805 9999 85.7143
+67 0.00857083 0.238836 0.477591 0.0717584 0.00890211 0.194341 9999 87.013
+68 0 0.299739 0.224789 0.162991 0 0.312481 9999 88.3117
+69 0.130471 0.00744875 0.142655 0.0797765 0.0144689 0.62518 9999 89.6104
+70 0 0.0885015 0.123175 0.0848114 0.154393 0.549119 9999 90.9091
+71 0.0193731 0.169013 0.294131 0.156181 0.168832 0.19247 9999 92.2078
+72 0.177202 0 0.0920932 0 0.233889 0.496817 9999 93.5065
+73 0 0.28753 0.31807 0.0945061 0.0438124 0.256081 9999 94.8052
+74 0.159814 0.161647 0.0858944 0.0236359 0.00712785 0.561881 9999 96.1039
+75 0.281868 0.152146 0.212211 0.0960142 0.0108111 0.246949 9999 97.4026
+76 0.0326215 0.136985 0.298295 0.0537373 0.0972424 0.381119 9999 98.7013
+77 0.140941 0.205805 0.148709 0.0279021 0.292366 0.184277 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_ye2026_sepsis_fewshot1.log

@@ -0,0 +1,126 @@
+>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
+>53146 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 31.564524356267
+>Best kappa: 31.564524356267 
+>SVD UpperRightDiag: 149239
+>SVD LowerRightDiag: 4728.05
+>=============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 0.037838 0.0831997 0.75208 0.0398659 0.0554681 0.0315483 9999 1.2987
+2 0.184585 0.0769089 0.254518 0.0913851 0.185574 0.207029 9999 2.5974
+3 0 0.0796359 0.0376797 0.378919 0.00890692 0.494858 9999 3.8961
+4 0 0.210598 0.259335 0.119667 0.0344169 0.375983 9999 5.19481
+5 0.56659 0 0 0 0 0.43341 9999 6.49351
+6 0.185023 0 0.20745 0.0318916 0.231115 0.34452 9999 7.79221
+7 0 0.055549 0.129004 0 0.0752916 0.740155 9999 9.09091
+8 0.0163099 0.0861974 0.518608 0.0392453 0.186595 0.153044 9999 10.3896
+9 0 0.0719086 0.143571 0.0395947 0.370969 0.373956 9999 11.6883
+10 0 0 0.608831 0.141435 0.00441107 0.245323 9999 12.987
+11 0 0 0.584124 0.17543 0.145974 0.094471 9999 14.2857
+12 0.0366093 0.0470545 0.53817 0.0872747 0.117436 0.173455 9999 15.5844
+13 0.0355765 0 0.552151 0.0940407 0.187492 0.13074 9999 16.8831
+14 0.133455 0.0303368 0.294905 0.218808 0.0220656 0.30043 9999 18.1818
+15 0.244985 0 0.0402838 0 0.00118547 0.713545 9999 19.4805
+16 0.31775 0.113775 0.347594 0.0587452 0.0374376 0.124699 9999 20.7792
+17 0.192172 0.0458658 0.225847 0.351634 0.0370301 0.147451 9999 22.0779
+18 0 0.144893 0.347333 0.108288 0.0530659 0.34642 9999 23.3766
+19 0.215184 0 0.484245 0.197577 0.0250081 0.0779863 9999 24.6753
+20 0.241365 0 0.439817 0.0551403 0.00932288 0.254356 9999 25.974
+21 0 0.0110841 0.63777 0.0461324 0.305013 0 9999 27.2727
+22 0 0.0571613 0.641849 0.124735 0.052368 0.123887 9999 28.5714
+23 0.0770421 0.252731 0.121923 0.106659 0.000302802 0.441342 9999 29.8701
+24 0.0783683 0.115986 0.0425823 0.319906 0 0.443158 9999 31.1688
+25 0.0627728 0.189386 0.190147 0.366129 0.000258787 0.191307 9999 32.4675
+26 0.0651895 0.133006 0.123716 0.247905 0 0.430183 9999 33.7662
+27 0.0651612 0.146766 0.0518584 0.311826 0.000177109 0.424211 9999 35.0649
+28 0.0575599 0.0734788 0.0663249 0.49568 0.000297617 0.306658 9999 36.3636
+29 0.108668 0.0211957 0.146813 0.162573 0.0739791 0.486771 9999 37.6623
+30 0.134363 0.0916226 0.196193 0.180458 0.00063787 0.396726 9999 38.961
+31 0.216671 0 0.486214 0.127594 0.0253621 0.14416 9999 40.2597
+32 0.124872 0.159001 0.368397 0.00992118 0.0542734 0.283535 9999 41.5584
+33 0 0.0984823 0.570714 0.118098 0.0389361 0.17377 9999 42.8571
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