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/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 143 mixture samples, 5927 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): 2351

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/fewshot4/out_fractions/.run.log

@@ -0,0 +1,192 @@
+>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
+>49194 DEG expressed across 6 samples were identified
+>Group size: 467, Kappa: 15.6425011742668
+>Best kappa: 15.6425011742668 
+>SVD UpperRightDiag: 64412.5
+>SVD LowerRightDiag: 4117.79
+>=============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 0.145835 0.00575728 0.66141 0.0928315 0.0220526 0.0721131 9999 0.699301
+2 0.121303 0 0.571691 0.202438 0.0149516 0.0896163 9999 1.3986
+3 0.0871589 0 0.199746 0 0.0484292 0.664666 9999 2.0979
+4 0.0689619 0 0.367839 0 0.110215 0.452984 9999 2.7972
+5 0.0681113 0 0.549725 0 0.11252 0.269643 9999 3.4965
+6 0.0444646 0.269229 0.26196 0.100131 0.0324556 0.291759 9999 4.1958
+7 0.0971285 0.10537 0.139551 0 0 0.65795 9999 4.8951
+8 0.0467795 0.200207 0.282898 0 0.0146354 0.45548 9999 5.59441
+9 0.0434651 0.181783 0.206753 0 0.0145541 0.553444 9999 6.29371
+10 0 0.23202 0.479651 0 0.0255697 0.262759 9999 6.99301
+11 0 0.358484 0.341407 0 0 0.300109 9999 7.69231
+12 0 0.321316 0.266724 0 0 0.41196 9999 8.39161
+13 0.0838089 0.0426746 0.513451 0.0913672 0.0201919 0.248506 9999 9.09091
+14 0 0.0822573 0.359068 0.161031 0.0527294 0.344915 9999 9.79021
+15 0.0516493 0.0707479 0.550252 0.0403567 0.0313944 0.2556 9999 10.4895
+16 0.104505 0 0.310351 0 0.0176973 0.567447 9999 11.1888
+17 0.143099 0 0.322287 0 0.0254272 0.509187 9999 11.8881
+18 0.140068 0.0314158 0.348953 0 0 0.479563 9999 12.5874
+19 0 0.0834794 0.403671 0.223001 0.0227621 0.267086 9999 13.2867
+20 0 0.0500171 0.594299 0.0469516 0.0411125 0.26762 9999 13.986
+21 0 0.143821 0.392206 0.078865 0.0608344 0.324274 9999 14.6853
+22 0 0.163104 0.331356 0.0365429 0.0222975 0.446699 9999 15.3846
+23 0 0.139316 0.291421 0.129959 0.0336354 0.405669 9999 16.0839
+24 0.00279684 0.188089 0.348426 0.0357786 0.0220877 0.402822 9999 16.7832
+25 0 0 0.328162 0.0391753 0.0122433 0.620419 9999 17.4825
+26 0.0802198 0 0.457031 0.060131 0.0492896 0.353329 9999 18.1818
+27 0.083908 0 0.296004 0 0.0360929 0.583995 9999 18.8811
+28 0.135506 0.0557283 0.272502 0.00942169 0.0445437 0.482299 9999 19.5804
+29 0.0608079 0 0.528116 0.281293 0.03104 0.0987425 9999 20.2797
+30 0.0402399 0 0.635253 0.175926 0.0337534 0.114827 9999 20.979
+31 0.0211716 0 0.389418 0.174827 0.134447 0.280137 9999 21.6783
+32 0.00457672 0.113604 0.434639 0.0213641 0.015266 0.41055 9999 22.3776
+33 0.0363054 0 0.470911 0 0.0148716 0.477912 9999 23.0769
+34 0 0.104079 0.486488 0.0143844 0.045355 0.349693 9999 23.7762
+35 0 0.190113 0.491565 0.12246 0 0.195862 9999 24.4755
+36 0.00993086 0.142839 0.401596 0.161468 0.0417435 0.242423 9999 25.1748
+37 0 0.212332 0.313682 0.182266 0.00856252 0.283158 9999 25.8741
+38 0.0249264 0 0.57772 0.0993421 0.084044 0.213968 9999 26.5734
+39 0 0 0.682281 0.0929108 0.0609926 0.163816 9999 27.2727
+40 0.0178264 0 0.535174 0 0.12895 0.318049 9999 27.972
+41 0.0403447 0 0.50243 0.00528352 0.123535 0.328406 9999 28.6713
+42 0.11056 0 0.505912 0.0663449 0.0423906 0.274793 9999 29.3706
+43 0.0456296 0 0.580288 0.0454063 0.0946248 0.234051 9999 30.0699
+44 0.111255 0.143569 0.26508 0.190045 0.0439879 0.246063 9999 30.7692
+45 0.0483754 0.204306 0.271057 0.24979 0.0288691 0.197603 9999 31.4685
+46 0 0.112422 0.293831 0.110235 0.0014701 0.482042 9999 32.1678
+47 0.0030812 0.172079 0.192999 0 0.0232909 0.60855 9999 32.8671
+48 0.0335814 0.0838607 0.555193 0.157785 0.0242729 0.145307 9999 33.5664
+49 0.0320962 0.0233806 0.461281 0.197198 0.041755 0.244288 9999 34.2657
+50 0.0128753 0.00960606 0.498804 0.13936 0.106429 0.232926 9999 34.965
+51 0.105717 0 0.683613 0 0.0229831 0.187687 9999 35.6643
+52 0.063264 0 0.348771 0.324717 0.20518 0.058068 9999 36.3636
+53 0.0139608 0 0.547023 0.169785 0.269231 0 9999 37.0629
+54 0.0239565 0 0.714758 0.0606793 0.092224 0.108383 9999 37.7622
+55 0.0768029 0 0.521682 0.171455 0.104346 0.125714 9999 38.4615
+56 0.0682442 0.0551155 0.407091 0.207673 0.128152 0.133725 9999 39.1608
+57 0.0498195 0.0402454 0.365197 0.138118 0.0901066 0.316514 9999 39.8601
+58 0.118476 0.166381 0.278687 0.0287943 0.0269466 0.380716 9999 40.5594
+59 0.106969 0.0815266 0.24933 0 0.031251 0.530924 9999 41.2587
+60 0.0896834 0.261773 0.165602 0.0973125 0.02814 0.357489 9999 41.958
+61 0 0 0.446494 0.173673 0.0965192 0.283313 9999 42.6573
+62 0.0492572 0.0774171 0.281477 0.261193 0.0253795 0.305277 9999 43.3566
+63 0.0357926 0.0783123 0.276182 0.266816 0.00815594 0.334741 9999 44.0559
+64 0.0490842 0.0613415 0.423152 0.16585 0 0.300572 9999 44.7552
+65 0.0140133 0.0367669 0.469314 0.158188 0.00116503 0.320553 9999 45.4545
+66 0 0.225826 0.257802 0.0680458 0 0.448326 9999 46.1538
+67 0.142941 0.0801921 0.134739 0.00851045 0 0.633618 9999 46.8531
+68 0.11075 0.108682 0.182754 0.128418 0 0.469396 9999 47.5524
+69 0.204551 0.0298937 0.152618 0 0 0.612937 9999 48.2517
+70 0 0.260009 0.372668 0.138058 0.000529638 0.228736 9999 48.951
+71 0.00084961 0.0245796 0.577109 0.252548 0.0749263 0.0699875 9999 49.6503
+72 0.0224664 0 0.865983 0.0666973 0.041563 0.00329029 9999 50.3497
+73 0.0522664 0.0745209 0.667986 0.0671092 0.0470412 0.0910762 9999 51.049
+74 0.0336282 0.0135487 0.759013 0.0177665 0.0772584 0.0987853 9999 51.7483
+75 0.354532 0.066739 0.159059 0 0 0.41967 9999 52.4476
+76 0.185074 0.100133 0.526066 0.0680855 0.000917063 0.119725 9999 53.1469
+77 0.31896 0.0228977 0.378534 0.141625 0.00978657 0.128197 9999 53.8462
+78 0.319439 0.0256464 0.238922 0.0650537 0.00091771 0.350022 9999 54.5455
+79 0.292739 0 0.16654 0.0906071 0.0311237 0.418989 9999 55.2448
+80 0.257722 0.128928 0.297528 0.068561 0 0.247261 9999 55.9441
+81 0.246436 0.0980231 0.26402 0.0452496 0 0.34627 9999 56.6434
+82 0.30479 0.0302206 0.283405 0.0108303 0.0173492 0.353405 9999 57.3427
+83 0 0 0.695516 0.0496374 0.152681 0.102166 9999 58.042
+84 0 0 0.566451 0.0445809 0.264581 0.124387 9999 58.7413
+85 0.0179321 0.0452681 0.607921 0.00891662 0.102372 0.21759 9999 59.4406
+86 0 0.0584902 0.484376 0.00602975 0.0584447 0.392659 9999 60.1399
+87 0.0649587 0.161053 0.19654 0.233888 0 0.34356 9999 60.8392
+88 0.123148 0.148593 0.187416 0.0525122 0.0145078 0.473823 9999 61.5385
+89 0.0515766 0.0708526 0.39573 0.247362 0.0556187 0.17886 9999 62.2378
+90 0.0456918 0 0.314604 0.342989 0.13487 0.161846 9999 62.9371
+91 0.110299 0 0.493371 0.211765 0.125147 0.0594185 9999 63.6364
+92 0.127669 0.125769 0.439536 0.118252 0.0741205 0.114653 9999 64.3357
+93 0.100391 0.111758 0.434779 0.141737 0.024439 0.186895 9999 65.035
+94 0.0142495 0.162889 0.231899 0.137433 0.00870333 0.444825 9999 65.7343
+95 0 0.0404451 0.462576 0.211441 0.00721251 0.278325 9999 66.4336
+96 0 0.0741412 0.361199 0.25011 0 0.314551 9999 67.1329
+97 0.0276143 0 0.581489 0.176757 0.0260948 0.188045 9999 67.8322
+98 0 0.037538 0.491821 0.172944 0.0448938 0.252803 9999 68.5315
+99 0.0442686 0 0.675005 0.11762 0.0269109 0.136196 9999 69.2308
+100 0.0931697 0.0195475 0.717562 0 0.00371291 0.166008 9999 69.9301
+101 0 0.136606 0.253541 0.0749032 0.0416573 0.493293 9999 70.6294
+102 0.129168 0.13241 0.277813 0.0631516 0.0199795 0.377477 9999 71.3287
+103 0.0322938 0.0262592 0.611123 0.169906 0.0523477 0.10807 9999 72.028
+104 0.0361717 0.10477 0.448793 0.105645 0.0835843 0.221036 9999 72.7273
+105 0.0761966 0 0.75206 0 0.00477624 0.166967 9999 73.4266
+106 0.0182142 0.181623 0.147597 0.0967909 0 0.555775 9999 74.1259
+107 0.00651693 0.0601829 0.174664 0.267082 0.000870255 0.490683 9999 74.8252
+108 0.136698 0.175903 0.287461 0.119034 0 0.280904 9999 75.5245
+109 0.201032 0.0672575 0.373744 0.158525 0.018317 0.181125 9999 76.2238
+110 0.101681 0.0782999 0.384751 0.247133 0.00198296 0.186152 9999 76.9231
+111 0.108267 0.079319 0.514732 0.117398 0.0112507 0.169032 9999 77.6224
+112 0.112714 0.159959 0.389651 0.0682887 0.0113304 0.258056 9999 78.3217
+113 0.0991343 0.145529 0.408607 0.174243 0.0215718 0.150915 9999 79.021
+114 0.0178498 0.163101 0.296828 0.126956 0.0620111 0.333255 9999 79.7203
+115 0.0674601 0.0676063 0.353334 0.151565 0.0228927 0.337142 9999 80.4196
+116 0.0525003 0.0498313 0.257195 0.337429 0.0243348 0.278709 9999 81.1189
+117 0.0435669 0.10773 0.188173 0.191323 0.0678702 0.401337 9999 81.8182
+118 0.0486458 0.0846869 0.156053 0.164707 0.126119 0.419788 9999 82.5175
+119 0.0132597 0.0717092 0.468511 0.176791 0.0440164 0.225712 9999 83.2168
+120 0.0278442 0 0.678476 0.208371 0.0261908 0.0591174 9999 83.9161
+121 0.0210119 0 0.734487 0.162156 0.0280867 0.0542583 9999 84.6154
+122 0.0876312 0.0738267 0.60165 0.152181 0.0847118 0 9999 85.3147
+123 0.0166612 0.0485464 0.588785 0.16631 0.0639294 0.115768 9999 86.014
+124 0.0227865 0.124937 0.449523 0.0855514 0.0823693 0.234833 9999 86.7133
+125 0.0480949 0.121928 0.669312 0.108275 0.0363108 0.0160791 9999 87.4126
+126 0.178175 0.0984042 0.605002 0.0552445 0.0218422 0.0413325 9999 88.1119
+127 0.357511 0.00598668 0.329328 0.104668 0.0247397 0.177767 9999 88.8112
+128 0.436215 0.0428692 0.253881 0.0367237 0.031188 0.199122 9999 89.5105
+129 0.350967 0.0604007 0.335404 0.0962557 0.0334537 0.123519 9999 90.2098
+130 0.212034 0.142997 0.459691 0.0772449 0.0221096 0.0859238 9999 90.9091
+131 0.173526 0.0580922 0.520627 0.0416464 0.0425461 0.163562 9999 91.6084
+132 0.222142 0.0548767 0.55291 0.0377946 0.0471708 0.085106 9999 92.3077
+133 0 0.234088 0.360587 0.0440926 0.0218483 0.339384 9999 93.007
+134 0.0177898 0.18098 0.117833 0.280763 0 0.402634 9999 93.7063
+135 0.0151203 0.0634743 0.410709 0.0801909 0.015643 0.414863 9999 94.4056
+136 0.0573364 0.241382 0.285449 0.0532691 0.0092241 0.353339 9999 95.1049
+137 0.0878759 0.162477 0.273202 0.0225534 0.0305018 0.423389 9999 95.8042
+138 0.00764523 0.162146 0.327905 0.101854 0.023067 0.377382 9999 96.5035
+139 0.0429827 0.10825 0.419019 0.154449 0.0263296 0.24897 9999 97.2028
+140 0.0374839 0.107298 0.340401 0 0.0140143 0.500803 9999 97.9021
+141 0.0219447 0.1138 0.379383 0.113569 0.000585264 0.370718 9999 98.6014
+142 0.0133893 0.110864 0.220331 0.0956945 0 0.559721 9999 99.3007
+143 0.0848167 0.196803 0.160011 0 0.0061171 0.552252 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv0/out_fractions/.run.log

@@ -0,0 +1,56 @@
+>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
+>50992 DEG expressed across 6 samples were identified
+>Group size: 499, Kappa: 10.8955797014857
+>Best kappa: 10.8955797014857 
+>SVD UpperRightDiag: 44968.1
+>SVD LowerRightDiag: 4127.19
+>=============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 0.0659631 0 0.206489 0.106881 0.62003 0.000636375 9999 14.2857
+2 0.0664402 0 0.294695 0.0677064 0.383451 0.187707 9999 28.5714
+3 0.0619614 0.0941273 0.177707 0.0922422 0.305689 0.268273 9999 42.8571
+4 0.043766 0.130443 0.156341 0.123794 0.260972 0.284684 9999 57.1429
+5 0.0469173 0.138396 0.0789841 0.0988704 0.609266 0.0275661 9999 71.4286
+6 0.0550578 0 0.163133 0.171844 0.452859 0.157106 9999 85.7143
+7 0.124364 0 0.210481 0.240939 0.352145 0.0720705 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv1/out_fractions/.run.log

@@ -0,0 +1,55 @@
+>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
+>52137 DEG expressed across 6 samples were identified
+>Group size: 500, Kappa: 17.5672909918671
+>Best kappa: 17.5672909918671 
+>SVD UpperRightDiag: 75546.6
+>SVD LowerRightDiag: 4300.41
+>=============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 0.12601 0.0327786 0.139898 0.0185195 0.305614 0.37718 9999 16.6667
+2 0.0863573 0.027406 0.169112 0.0586599 0.463835 0.19463 9999 33.3333
+3 0.0284826 0.0506041 0.0861528 0.174771 0.165772 0.494218 9999 50
+4 0.0763762 0.00483459 0.116828 0.0685603 0.569667 0.163733 9999 66.6667
+5 0.0770127 0.0507759 0.0853344 0.101742 0.572851 0.112284 9999 83.3333
+6 0.0810219 0 0.367215 0.0568868 0.266946 0.227931 9999 100