Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot2/out_fractions/.run.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
+>53923 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 11.844165798807
+>Best kappa: 11.844165798807 
+>SVD UpperRightDiag: 53643.2
+>SVD LowerRightDiag: 4529.08
+>=============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 0.0505484 0.139776 0.675146 0.0438243 0.0544997 0.0362055 9999 1.2987
+2 0.294341 0 0.236895 0.0921395 0.187621 0.189003 9999 2.5974
+3 0.00951439 0.0730371 0.0156729 0.439701 0.00526814 0.456807 9999 3.8961
+4 0.0964799 0.154122 0.223073 0.127924 0.0492713 0.34913 9999 5.19481
+5 0.597234 0 0 0 0 0.402766 9999 6.49351
+6 0.243998 0 0.175646 0.000816 0.263361 0.316179 9999 7.79221
+7 0 0.0805716 0.0751382 0 0.0287837 0.815506 9999 9.09091
+8 0.0997302 0 0.511189 0.0462623 0.202913 0.139906 9999 10.3896
+9 0 0.0600501 0.167377 0.045546 0.299283 0.427743 9999 11.6883
+10 0.0827205 0 0.518646 0.154841 0.0274696 0.216324 9999 12.987
+11 0.0733926 0.0333938 0.537658 0.182156 0.078559 0.0948404 9999 14.2857
+12 0.0275234 0.0477775 0.561338 0.0961943 0.0765829 0.190584 9999 15.5844
+13 0.0385449 0 0.616681 0.0936274 0.0899732 0.161173 9999 16.8831
+14 0.0317308 0.0738412 0.302927 0.23779 0.03874 0.314971 9999 18.1818
+15 0.199051 0.0167695 0.0206752 0.00853269 0.00113003 0.753841 9999 19.4805
+16 0.241334 0.190864 0.276551 0.0802855 0.0748067 0.136158 9999 20.7792
+17 0.135003 0.0766263 0.216512 0.381958 0.0418339 0.148067 9999 22.0779
+18 0 0.148232 0.340969 0.136456 0.0760368 0.298306 9999 23.3766
+19 0.0993658 0 0.562038 0.214823 0.0291577 0.094615 9999 24.6753
+20 0.113903 0.0526999 0.456883 0.0626528 0.0259828 0.287879 9999 25.974
+21 0 0.108426 0.624396 0.0417323 0.19531 0.0301355 9999 27.2727
+22 0.00267816 0.00324082 0.660842 0.159138 0.0645066 0.109595 9999 28.5714
+23 0.0964797 0.284685 0.0655468 0.143039 0.00966808 0.400581 9999 29.8701
+24 0.101499 0.0996736 0.0256091 0.349102 0 0.424117 9999 31.1688
+25 0.0480127 0.237095 0.16556 0.399515 0.00224312 0.147575 9999 32.4675
+26 0.0150163 0.19348 0.0496873 0.306083 0 0.435734 9999 33.7662
+27 0.0505611 0.173092 0.0639603 0.34404 0.011242 0.357104 9999 35.0649
+28 0.0976079 0.0946115 0.065666 0.355256 0.00881188 0.378047 9999 36.3636
+29 0.0358899 0.128898 0.00325549 0.581776 0.00241742 0.247764 9999 37.6623
+30 0.0971051 0.0248864 0.150415 0.179771 0.0734095 0.474413 9999 38.961
+31 0.041325 0.215515 0.13847 0.2263 0.00151977 0.376871 9999 40.2597
+32 0.131631 0 0.550414 0.140781 0.0342581 0.142915 9999 41.5584
+33 0.0559195 0.195596 0.366784 0.0382444 0.0800256 0.263431 9999 42.8571
+34 0 0.157618 0.509994 0.10413 0.0495982 0.178659 9999 44.1558
+35 0.105879 0.127286 0.278764 0 0.0715569 0.416514 9999 45.4545
+36 0.1685 0.133359 0.0102063 0.193001 0.0077481 0.487186 9999 46.7532
+37 0.256587 0.0588978 0.0864022 0.0755663 0.00153108 0.521016 9999 48.0519
+38 0.209136 0.0758254 0 0.0795515 0 0.635487 9999 49.3506
+39 0.0815794 0.185924 0.0735339 0.123903 0.0106807 0.524379 9999 50.6494
+40 0.40454 0.0849866 0.0227087 0.0610262 0.00358686 0.423152 9999 51.9481
+41 0.111379 0.037004 0.480138 0.0413812 0.0133183 0.316779 9999 53.2468
+42 0.20479 0.130937 0.163133 0 0.00215229 0.498987 9999 54.5455
+43 0.156354 0 0.188006 0.0517183 0.0155173 0.588404 9999 55.8442
+44 0.346086 0.0305674 0.388518 0 0.0158075 0.21902 9999 57.1429
+45 0.285084 0 0.311192 0 0.00502283 0.398702 9999 58.4416
+46 0.222343 0.0050707 0 0 0 0.772586 9999 59.7403
+47 0.0898013 0.0721609 0.292214 0.192233 0.102126 0.251465 9999 61.039
+48 0.0276762 0.184599 0.310434 0.102685 0 0.374606 9999 62.3377
+49 0.388758 0.0261971 0.0746656 0 0 0.51038 9999 63.6364
+50 0.183372 0 0.0973772 0 0 0.71925 9999 64.9351
+51 0.00905965 0.0192364 0.0747446 0.0189198 0.17345 0.704589 9999 66.2338
+52 0.155551 0 0.249872 0.226954 0 0.367622 9999 67.5325
+53 0.0116157 0.16637 0.498032 0.0734579 0.0364955 0.214029 9999 68.8312
+54 0 0.0824646 0.413097 0.391188 0 0.11325 9999 70.1299
+55 0.0751274 0.0800749 0.373648 0.054174 0.0216985 0.395278 9999 71.4286
+56 0.0503289 0.0899242 0.519534 0.118461 0.0159502 0.205802 9999 72.7273
+57 0.116156 0.141809 0.420009 0.133926 0.145486 0.0426142 9999 74.026
+58 0.11278 0.166326 0.0139207 0.170235 0.0115231 0.525216 9999 75.3247
+59 0.193711 0 0.427472 0.0825145 0.00871097 0.287591 9999 76.6234
+60 0.0625002 0.112937 0.122993 0.0926252 0.0764652 0.532479 9999 77.9221
+61 0.0999929 0 0.377722 0.256499 0.0283055 0.237481 9999 79.2208
+62 0 0.052052 0.231098 0.228059 0.155199 0.333591 9999 80.5195
+63 0.0941159 0 0.316861 0.16579 0.072507 0.350727 9999 81.8182
+64 0.0679843 0.119838 0.246579 0.115709 0.0470174 0.402873 9999 83.1169
+65 0 0.234738 0.310185 0.194568 0.10519 0.155319 9999 84.4156
+66 0.164856 0 0.478354 0.0706489 0.0783411 0.207801 9999 85.7143
+67 0.0296771 0.147138 0.590738 0.0700124 0.00996005 0.152474 9999 87.013
+68 0.0151568 0.22638 0.292791 0.148591 0 0.317082 9999 88.3117
+69 0.0947341 0 0.134619 0.103248 0.00816069 0.659239 9999 89.6104
+70 0 0.0767485 0.182445 0.0683586 0.125139 0.547308 9999 90.9091
+71 0 0.0387716 0.410116 0.13152 0.188339 0.231253 9999 92.2078
+72 0.111132 0.00447745 0.0816682 0 0.246022 0.5567 9999 93.5065
+73 0.0347788 0.18533 0.378896 0.101883 0.057518 0.241594 9999 94.8052
+74 0.177612 0.0532406 0.147104 0.0690292 0.0111708 0.541844 9999 96.1039
+75 0.22556 0.103433 0.282239 0.103415 0.00967482 0.275677 9999 97.4026
+76 0.0238069 0.0387648 0.362994 0.0616973 0.0996089 0.413128 9999 98.7013
+77 0.123799 0.0940741 0.258885 0.0288173 0.270795 0.223629 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot3/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 77 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 24
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 1108

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot3/out_fractions/.run.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
+>51845 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 31.350059311153
+>Best kappa: 31.350059311153 
+>SVD UpperRightDiag: 122213
+>SVD LowerRightDiag: 3898.32
+>=============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 0.0771013 0.150356 0.6249 0.0472548 0.0604626 0.0399248 9999 1.2987
+2 0.404686 0.0118999 0.1732 0.0960374 0.19573 0.118446 9999 2.5974
+3 0.0123272 0.0753995 0.0304863 0.398649 0.00509537 0.478042 9999 3.8961
+4 0.114453 0.16124 0.176621 0.125863 0.054779 0.367044 9999 5.19481
+5 0.593375 0 0 0 0 0.406625 9999 6.49351
+6 0.347678 0 0.13114 0.0102637 0.239403 0.271515 9999 7.79221
+7 0.0180789 0.0235159 0.0805887 0 0.0970939 0.780723 9999 9.09091
+8 0.142158 0.108073 0.373452 0.0470327 0.197029 0.132255 9999 10.3896
+9 0.0820638 0 0.152256 0.0459038 0.456941 0.262836 9999 11.6883
+10 0.0814997 0.123908 0.380086 0.15016 0.0269387 0.237408 9999 12.987
+11 0.0795608 0.0984607 0.413044 0.188021 0.154698 0.0662152 9999 14.2857
+12 0.0102912 0.16332 0.437 0.0904302 0.149314 0.149645 9999 15.5844
+13 0.0588152 0.00095797 0.485981 0.126756 0.221648 0.105843 9999 16.8831
+14 0 0.131142 0.178442 0.282412 0.0313268 0.376677 9999 18.1818
+15 0.165157 0.0191662 0.0249224 0 0.00137086 0.789384 9999 19.4805
+16 0.189336 0.193544 0.271042 0.0900067 0.0478009 0.208271 9999 20.7792
+17 0.084277 0.143078 0.157858 0.404472 0.0391313 0.171184 9999 22.0779
+18 0.108927 0.032058 0.427707 0.265033 0.0283418 0.137933 9999 23.3766
+19 0.10162 0.0708579 0.407813 0.0662595 0.00899628 0.344453 9999 24.6753
+20 0.0123592 0.162174 0.399995 0.0991226 0.326349 0 9999 25.974
+21 0.0059483 0.169213 0.428392 0.199376 0.0734874 0.123584 9999 27.2727
+22 0.0427796 0.354275 0.0156185 0.136878 0.000275362 0.450174 9999 28.5714
+23 0.0777141 0.130944 0 0.330769 0 0.460573 9999 29.8701
+24 0.000185733 0.321931 0.0531197 0.430579 0.000178605 0.194006 9999 31.1688
+25 0.0278641 0.202189 0.0262778 0.271507 0 0.472162 9999 32.4675
+26 0.012321 0.220998 0.00943719 0.337818 0.000165056 0.419261 9999 33.7662
+27 0.0697432 0.157799 0.00719268 0.324781 0.00015535 0.440329 9999 35.0649
+28 0.00283812 0.155119 0 0.579458 0.000300839 0.262284 9999 36.3636
+29 0.092465 0.0870889 0.0471963 0.187074 0.0865295 0.499647 9999 37.6623
+30 0 0.24891 0.0723301 0.24295 0.000596043 0.435214 9999 38.961
+31 0.127847 0.0364763 0.437315 0.189153 0.037755 0.171453 9999 40.2597
+32 0.0429669 0.279587 0.285785 0.0410044 0.0765554 0.274102 9999 41.5584
+33 0.00555556 0.274593 0.354684 0.13608 0.0465487 0.18254 9999 42.8571
+34 0.100708 0.193747 0.180174 0 0.0620068 0.463365 9999 44.1558
+35 0.200157 0.123354 0.0109376 0.171632 0.000663296 0.493256 9999 45.4545
+36 0.283385 0.107516 0.0328325 0.0516908 1.98911e-05 0.524556 9999 46.7532
+37 0.217171 0.0895035 0 0.0630614 0 0.630264 9999 48.0519
+38 0.0458516 0.0792519 0.0260051 0.0779563 0.021934 0.749001 9999 49.3506
+39 0.481463 0.0631519 0.0139581 0.0567185 0.000772101 0.383936 9999 50.6494
+40 0.0756641 0.088992 0.438354 0.0084754 0.00876686 0.379748 9999 51.9481
+41 0.220421 0.148947 0.123902 0 0.00410498 0.502625 9999 53.2468
+42 0.199391 0 0.115622 0.0419804 0.0671509 0.575856 9999 54.5455
+43 0.389928 0.171706 0.24627 0.00553533 0.0170624 0.169498 9999 55.8442
+44 0.376558 0 0.246932 0 0.0496969 0.326813 9999 57.1429
+45 0.267482 0 0.00210572 0 0.032642 0.69777 9999 58.4416
+46 0.127743 0.0383791 0.289203 0.204541 0.1001 0.240034 9999 59.7403
+47 0.0165695 0.197278 0.286856 0.0918321 0 0.407464 9999 61.039
+48 0.376094 0.035162 0.0531746 0 0.00275708 0.532812 9999 62.3377
+49 0.205471 0 0.0924906 0 0 0.702039 9999 63.6364
+50 0.0267435 0 0.0841789 0 0.195993 0.693085 9999 64.9351
+51 0.170409 0 0.227416 0.208909 0.0197098 0.373557 9999 66.2338
+52 0 0.312607 0.323315 0.0695301 0.0239158 0.270632 9999 67.5325
+53 0 0.310694 0.325415 0.00905525 0.00122042 0.353615 9999 68.8312
+54 0.0559916 0.0960511 0.333914 0.0380301 0.012154 0.463859 9999 70.1299
+55 0.0271532 0.18278 0.340723 0.148045 0.0143069 0.286992 9999 71.4286
+56 0.103208 0.138509 0.466824 0.136747 0.142262 0.0124494 9999 72.7273
+57 0.112855 0.155163 0.0474411 0.149856 0.00464208 0.530043 9999 74.026
+58 0.131448 0.00765527 0.435933 0.0656731 0.000340808 0.35895 9999 75.3247
+59 0.242022 0.0407884 0.0605136 0.143979 7.61301e-05 0.512621 9999 76.6234
+60 0.086186 0 0.356316 0.302838 0.0269834 0.227676 9999 77.9221
+61 0.0282363 0.0791456 0.14235 0.264361 0.174603 0.311304 9999 79.2208
+62 0.110859 0 0.290445 0.170182 0.0762834 0.35223 9999 80.5195
+63 0.121074 0.150152 0.150458 0.124541 0.0464646 0.407311 9999 81.8182
+64 0.0745415 0.0147251 0.456983 0 0.11818 0.33557 9999 83.1169
+65 0 0.263305 0.247039 0.213922 0.112814 0.16292 9999 84.4156
+66 0.198447 0 0.382531 0.0781735 0.177754 0.163094 9999 85.7143
+67 0.0304581 0.263567 0.222394 0.155692 0.000335573 0.327553 9999 87.013
+68 0.0915328 0.0142415 0.127655 0.071386 0.00905196 0.686133 9999 88.3117
+69 0.0102124 0.0665446 0.10416 0.0430258 0.261052 0.515006 9999 89.6104
+70 0.0430018 0.112558 0.253899 0.201495 0.217836 0.17121 9999 90.9091
+71 0.206577 0 0.0839693 0 0.233363 0.476091 9999 92.2078
+72 0.0238915 0.0107257 0.0088077 0.338016 0.000329837 0.618229 9999 93.5065
+73 0.0283796 0.152272 0.322338 0.12876 0.0560507 0.3122 9999 94.8052
+74 0.12596 0.129271 0.0827587 0.0345197 0.0182639 0.609227 9999 96.1039
+75 0.205652 0.18755 0.180556 0.112253 0.00881771 0.305171 9999 97.4026
+76 0.0438634 0.0814319 0.273061 0.0494294 0.187554 0.364661 9999 98.7013
+77 0.193717 0.104744 0.194344 0.0308311 0.312452 0.163911 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot4/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 77 mixture samples, 5975 genes, and 6 cell subsets...
+>Window size adaptively set to 24
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 1077