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/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 142 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): 2309

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

@@ -0,0 +1,191 @@
+>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
+>49689 DEG expressed across 6 samples were identified
+>Group size: 496, Kappa: 23.5800000287385
+>Best kappa: 23.5800000287385 
+>SVD UpperRightDiag: 110120
+>SVD LowerRightDiag: 4670.04
+>=============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 0.185215 0.0117177 0.601768 0.0915209 0.0370983 0.0726805 9999 0.704225
+2 0.192642 0 0.481965 0.219813 0.033539 0.072041 9999 1.40845
+3 0.154367 0 0.174116 0 0.0817163 0.589801 9999 2.11268
+4 0.20926 0 0.321914 0 0.148052 0.320775 9999 2.8169
+5 0.133506 0 0.469356 0 0.188298 0.208839 9999 3.52113
+6 0.0965382 0.248737 0.179323 0.112528 0.0598666 0.303007 9999 4.22535
+7 0.143381 0.0847765 0.1226 0.0299973 0.0268237 0.592422 9999 4.92958
+8 0.070229 0.189905 0.217116 0.0571743 0.0432406 0.422335 9999 5.6338
+9 0.0424047 0.16998 0.176474 0.013919 0.0512577 0.545965 9999 6.33803
+10 0 0.045193 0.425943 0.410767 0.0612262 0.056871 9999 7.04225
+11 0.0127205 0 0.479351 0.445768 0.0621599 0 9999 7.74648
+12 0.013406 0 0.405694 0.457738 0.0893822 0.03378 9999 8.4507
+13 0.0248668 0.194445 0.450379 0 0.0758244 0.254485 9999 9.15493
+14 0 0.357979 0.283819 0 0.0304883 0.327713 9999 9.85915
+15 0 0.313781 0.213641 0.0294303 0.0235185 0.419629 9999 10.5634
+16 0.0956651 0.0532265 0.347007 0.0481893 0.0476666 0.408245 9999 11.2676
+17 0.129751 0.05381 0.245266 0.0571237 0.0622551 0.451794 9999 11.9718
+18 0.0614974 0.126514 0.259805 0.0679519 0.0566651 0.427566 9999 12.6761
+19 0.108986 0.0400498 0.452556 0.0690969 0.0497341 0.279577 9999 13.3803
+20 0.143058 0.0195625 0.299629 0.165873 0.0919968 0.279881 9999 14.0845
+21 0.086544 0.0426666 0.481374 0.0769584 0.0792756 0.233181 9999 14.7887
+22 0.13903 0 0.293321 0 0.0410411 0.526607 9999 15.493
+23 0.0909983 0.0124233 0.296552 0 0.0374262 0.5626 9999 16.1972
+24 0.086658 0.113356 0.306526 0.0237227 0.00403487 0.465703 9999 16.9014
+25 0.0426814 0.0397212 0.387487 0.270297 0.0527372 0.207076 9999 17.6056
+26 0.0148078 0.0356532 0.523111 0.0949816 0.0890668 0.242379 9999 18.3099
+27 0.0331576 0.0888953 0.349993 0.117509 0.109345 0.301099 9999 19.0141
+28 0.036553 0.143721 0.285567 0.108183 0.0577754 0.368201 9999 19.7183
+29 0.00873494 0.13518 0.215402 0.18247 0.0645738 0.393639 9999 20.4225
+30 0.00732363 0.177075 0.297597 0.0514219 0.0501016 0.41648 9999 21.1268
+31 0.0850577 0 0.411219 0.107496 0.0998795 0.296348 9999 21.831
+32 0.0868381 0 0.279196 0.0826787 0.0837151 0.467573 9999 22.5352
+33 0.115709 0.0450787 0.247541 0.0444184 0.0843607 0.462892 9999 23.2394
+34 0.101324 0 0.474699 0.260608 0.0517499 0.111619 9999 23.9437
+35 0.128271 0 0.565324 0.157527 0.0514437 0.0974342 9999 24.6479
+36 0.143586 0 0.311265 0.182559 0.170274 0.192316 9999 25.3521
+37 0.00960736 0.12096 0.359546 0.0776508 0.0522991 0.379936 9999 26.0563
+38 0.0453152 0 0.416381 0.0157432 0.0501487 0.472412 9999 26.7606
+39 0.0685147 0.133871 0.454027 0.166859 0.0188748 0.157854 9999 27.4648
+40 0.00996971 0.1829 0.331815 0.205163 0.0788779 0.191274 9999 28.169
+41 0.00705598 0.200933 0.253939 0.199022 0.0430991 0.295951 9999 28.8732
+42 0.0975246 0.167554 0.205954 0.187543 0.0745001 0.266924 9999 29.5775
+43 0.023296 0.313682 0.172635 0.241365 0.0576446 0.191377 9999 30.2817
+44 0.0408116 0.0749019 0.260614 0.149001 0.0291202 0.445551 9999 30.9859
+45 0.00110177 0.162719 0.138482 0.0646895 0.0551181 0.577889 9999 31.6901
+46 0.0108038 0.191374 0.444766 0.178928 0.0564336 0.117694 9999 32.3944
+47 0.0522016 0.0189771 0.448209 0.202908 0.0633005 0.214404 9999 33.0986
+48 0.0540353 0 0.442438 0.151368 0.150783 0.201376 9999 33.8028
+49 0.106753 0 0.692002 0 0.0679941 0.133251 9999 34.507
+50 0.0915189 0 0.318154 0.279895 0.260316 0.0501158 9999 35.2113
+51 0.0195861 0 0.451988 0.164247 0.364179 0 9999 35.9155
+52 0.0709492 0 0.658044 0.0733669 0.121537 0.0761028 9999 36.6197
+53 0.133964 0 0.477228 0.15833 0.1374 0.0930783 9999 37.3239
+54 0.121204 0.0124522 0.348457 0.200342 0.195367 0.122178 9999 38.0282
+55 0.0608996 0.052998 0.288196 0.167747 0.136851 0.293309 9999 38.7324
+56 0.112617 0.134897 0.234182 0.0852296 0.0628781 0.370195 9999 39.4366
+57 0.117974 0.11392 0.208936 0.0767219 0.0700314 0.412417 9999 40.1408
+58 0.0779508 0.223667 0.126934 0.140525 0.0601391 0.370784 9999 40.8451
+59 0.108678 0 0.385503 0.197534 0.132284 0.176 9999 41.5493
+60 0.0953668 0.0533766 0.261239 0.33628 0.0560761 0.197661 9999 42.2535
+61 0.0503485 0.0667794 0.238721 0.302048 0.0314741 0.310629 9999 42.9577
+62 0.0589621 0.0543709 0.40357 0.163621 0.00656213 0.312913 9999 43.662
+63 0.124926 0 0.382315 0.191199 0.0153032 0.286257 9999 44.3662
+64 0.0605274 0.189894 0.224446 0.0961492 0 0.428984 9999 45.0704
+65 0.166626 0.0604879 0.134717 0.136572 0 0.501597 9999 45.7746
+66 0.119915 0.125636 0.160919 0.208276 0.0143437 0.370911 9999 46.4789
+67 0.198279 0.0414402 0.136298 0.0381843 0.00972818 0.576069 9999 47.1831
+68 0.097126 0.162977 0.280368 0.137008 0.0150006 0.307521 9999 47.8873
+69 0.0989163 0.129502 0.373557 0.0624017 0.10477 0.230852 9999 48.5915
+70 0.0207741 0.189279 0.334792 0.188957 0.0361258 0.230073 9999 49.2958
+71 0.0130177 0.00939411 0.553077 0.218957 0.12245 0.083104 9999 50
+72 0.0353375 0 0.808172 0.0697556 0.0865386 0.000196294 9999 50.7042
+73 0.12102 0 0.606236 0.0979602 0.0989597 0.0758237 9999 51.4085
+74 0.0495202 0 0.689117 0.040559 0.12738 0.093423 9999 52.1127
+75 0.312392 0.117488 0.128603 0.0336334 0.0187554 0.389128 9999 52.8169
+76 0.175378 0.15047 0.446733 0.0943033 0.0167354 0.116381 9999 53.5211
+77 0.262522 0.155318 0.32445 0.167132 0.00281265 0.0877659 9999 54.2254
+78 0.200243 0.148338 0.211789 0.117054 0.00740874 0.315167 9999 54.9296
+79 0.240062 0.0416778 0.133795 0.142199 0.0561364 0.38613 9999 55.6338
+80 0.241336 0.174809 0.260305 0.113608 0.0117874 0.198154 9999 56.338
+81 0.235373 0.139583 0.221891 0.110452 0.0106835 0.282017 9999 57.0423
+82 0.193845 0.143764 0.237094 0.0497915 0.0372894 0.338217 9999 57.7465
+83 0.0103126 0.00455493 0.601613 0.0748953 0.230528 0.0780956 9999 58.4507
+84 0.022695 0 0.492262 0.0517307 0.337446 0.0958663 9999 59.1549
+85 0.094497 0.0164704 0.550328 0.0462619 0.144779 0.147664 9999 59.8592
+86 0.0484495 0.0424189 0.387406 0.0899889 0.119227 0.31251 9999 60.5634
+87 0.0439603 0.190758 0.122624 0.25539 0.0252799 0.361988 9999 61.2676
+88 0.111324 0.165489 0.13353 0.0784804 0.0371326 0.474044 9999 61.9718
+89 0.0866415 0.052322 0.379047 0.255352 0.0993422 0.127295 9999 62.6761
+90 0.124074 0 0.277266 0.286228 0.171592 0.14084 9999 63.3803
+91 0.185537 0 0.437503 0.160379 0.152514 0.0640678 9999 64.0845
+92 0.190665 0.0879468 0.38298 0.0967059 0.118437 0.123265 9999 64.7887
+93 0.139598 0.0845336 0.38222 0.132324 0.0491747 0.21215 9999 65.493
+94 0.0422561 0.120231 0.210534 0.21688 0.0327887 0.377311 9999 66.1972
+95 0.0130229 0.0326128 0.435734 0.302098 0.0263947 0.190138 9999 66.9014
+96 0.00574495 0.0640603 0.315735 0.31186 0.0126056 0.289995 9999 67.6056
+97 0.0310228 0 0.537531 0.205075 0.0542364 0.172136 9999 68.3099
+98 0.0352967 0.0124711 0.42395 0.226908 0.0793092 0.222065 9999 69.0141
+99 0.116131 0 0.586059 0.139846 0.0567764 0.101188 9999 69.7183
+100 0.166461 0 0.637774 0.0145982 0.0312504 0.149917 9999 70.4225
+101 0.0402946 0.0864387 0.222581 0.169508 0.0869565 0.394221 9999 71.1268
+102 0.0816696 0.168716 0.217391 0.0750293 0.0498005 0.407393 9999 71.831
+103 0.0389384 0.0165761 0.574897 0.169322 0.0947119 0.105554 9999 72.5352
+104 0.0398072 0.110101 0.393044 0.141639 0.11737 0.198039 9999 73.2394
+105 0.0208569 0.0606515 0.0312282 0.380843 0 0.50642 9999 73.9437
+106 0.0612466 0 0.751979 0 0.0185131 0.168261 9999 74.6479
+107 0.0546537 0.0308649 0.156068 0.287558 0.0170223 0.453833 9999 75.3521
+108 0.121877 0.226153 0.2066 0.172272 0.0079381 0.265159 9999 76.0563
+109 0.113391 0.154601 0.327468 0.129779 0.0369942 0.237767 9999 76.7606
+110 0.0915853 0.126029 0.342238 0.274969 0.00832337 0.156856 9999 77.4648
+111 0.182112 0.0774008 0.44094 0.139765 0.0340311 0.125752 9999 78.169
+112 0.178644 0.149352 0.291906 0.123706 0.0373691 0.219023 9999 78.8732
+113 0.057761 0.195719 0.343343 0.214462 0.0482946 0.14042 9999 79.5775
+114 0.0239886 0.154697 0.244261 0.1462 0.106648 0.324206 9999 80.2817
+115 0.0592911 0.0763117 0.29272 0.158326 0.0416224 0.371729 9999 80.9859
+116 0.0841667 0.042242 0.219749 0.34771 0.0496148 0.256518 9999 81.6901
+117 0.0833747 0.094117 0.143085 0.241071 0.10404 0.334312 9999 82.3944
+118 0.0990791 0.0620201 0.12194 0.233028 0.166238 0.317694 9999 83.0986
+119 0.0101961 0.166259 0.139493 0.25561 0 0.428443 9999 83.8028
+120 0.0355933 0.0719963 0.243664 0.343388 0.0185686 0.28679 9999 84.507
+121 0.139234 0.0537761 0.11456 0.245847 0.0394102 0.407173 9999 85.2113
+122 0.0971612 0.0663052 0.107098 0.311269 0.0709292 0.347237 9999 85.9155
+123 0.000562843 0.114365 0.0858169 0.30773 0.0476154 0.443911 9999 86.6197
+124 0.0664996 0.133711 0.576095 0.103413 0.0715562 0.0487256 9999 87.3239
+125 0.219895 0.100305 0.527907 0.0698143 0.050706 0.031372 9999 88.0282
+126 0.374218 0.0229476 0.25202 0.0874596 0.0490826 0.214273 9999 88.7324
+127 0.566895 0 0.204959 0.0615312 0.0525475 0.114068 9999 89.4366
+128 0.390326 0.0432978 0.284708 0.117993 0.0702035 0.093472 9999 90.1408
+129 0.289115 0.0801225 0.385407 0.0856434 0.0609272 0.0987849 9999 90.8451
+130 0.249716 0.0334624 0.431032 0.0820452 0.0811512 0.122593 9999 91.5493
+131 0.229062 0.064562 0.446151 0.0417922 0.0811507 0.137282 9999 92.2535
+132 0.0552588 0.188316 0.301317 0.113617 0.0501502 0.291341 9999 92.9577
+133 0.0308115 0.155855 0.102686 0.31628 0.0191679 0.375199 9999 93.662
+134 0.0351244 0.05733 0.359502 0.139301 0.0545404 0.354203 9999 94.3662
+135 0.0562671 0.251788 0.194908 0.118566 0.0333718 0.345099 9999 95.0704
+136 0.0645736 0.147315 0.215294 0.0511158 0.070518 0.451184 9999 95.7746
+137 0.013711 0.171016 0.245267 0.1801 0.0532097 0.336697 9999 96.4789
+138 0.0394656 0.110224 0.375829 0.189709 0.0549666 0.229806 9999 97.1831
+139 0.0229709 0.0881049 0.298922 0.0181511 0.0426982 0.529153 9999 97.8873
+140 0.0140083 0.129074 0.285928 0.153347 0.0150653 0.402578 9999 98.5915
+141 0.00564523 0.120957 0.154976 0.108471 0.0117319 0.598218 9999 99.2958
+142 0.0873778 0.170382 0.151628 0 0.0242565 0.566355 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/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 145 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): 2384

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/imperial_eskd/fewshot3/out_fractions/.run.log

@@ -0,0 +1,194 @@
+>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
+>51359 DEG expressed across 6 samples were identified
+>Group size: 496, Kappa: 9.29421809349584
+>Best kappa: 9.29421809349584 
+>SVD UpperRightDiag: 46513.4
+>SVD LowerRightDiag: 5004.56
+>=============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 0.118925 0.0565716 0.589665 0.113265 0.0246633 0.09691 9999 0.689655
+2 0.0991112 0.00723543 0.528262 0.246048 0.0228456 0.0964973 9999 1.37931
+3 0.0474866 0.0361636 0.146005 0 0.0491583 0.721186 9999 2.06897
+4 0 0.0106725 0.348363 0 0.123578 0.517387 9999 2.75862
+5 0.0283468 0.00134061 0.500257 0 0.125451 0.344605 9999 3.44828
+6 0.00756829 0.241582 0.230023 0.120723 0.0332846 0.366818 9999 4.13793
+7 0 0.0890169 0.425809 0.378753 0.0416781 0.0647426 9999 4.82759
+8 0 0 0.506146 0.424905 0.0394769 0.0294724 9999 5.51724
+9 0 0.0168479 0.426211 0.421817 0.0791341 0.0559901 9999 6.2069
+10 0 0.25612 0.4156 0 0.0327587 0.295521 9999 6.89655
+11 0 0.320632 0.277249 0 0.0094243 0.392695 9999 7.58621
+12 0 0.338924 0.211284 0.0261645 0.000109704 0.423518 9999 8.27586
+13 0 0.119197 0.363003 0.0230311 0.0254485 0.46932 9999 8.96552
+14 0 0.0848823 0.272348 0.0323178 0.043207 0.567245 9999 9.65517
+15 0 0.162152 0.266064 0.0480365 0.0214601 0.502288 9999 10.3448
+16 0.0348482 0 0.276829 0.0192014 0.0197078 0.649414 9999 11.0345
+17 0.0192355 0.0511904 0.23856 0 0.0162618 0.674752 9999 11.7241
+18 0.0569338 0.100317 0.29375 0 0 0.548998 9999 12.4138
+19 0 0.10782 0.345363 0.235177 0.0258273 0.285814 9999 13.1034
+20 0 0.0628567 0.520847 0.11299 0.0619072 0.241399 9999 13.7931
+21 0 0.132008 0.357611 0.120164 0.0699417 0.320275 9999 14.4828
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