Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/cv0/hires_run.log

@@ -0,0 +1,12 @@
+>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
+CIBERSORTxHiRes: /src/src/../include/Eigen/src/Core/Product.h:97: Eigen::Product<Lhs, Rhs, Option>::Product(const Lhs&, const Rhs&) [with _Lhs = Eigen::Matrix<double, -1, -1>; _Rhs = Eigen::Matrix<double, -1, 1>; int Option = 0; Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Matrix<double, -1, -1>; Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Matrix<double, -1, 1>]: Assertion `lhs.cols() == rhs.rows() && "invalid matrix product" && "if you wanted a coeff-wise or a dot product use the respective explicit functions"' failed.
+qemu: uncaught target signal 6 (Aborted) - core dumped

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/cv1/out_fractions/.run.log

@@ -0,0 +1,54 @@
+>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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>45154 DEG expressed across 6 samples were identified
+>Group size: 452, Kappa: 12.5438145603335
+>Best kappa: 12.5438145603335 
+>SVD UpperRightDiag: 62840.9
+>SVD LowerRightDiag: 5009.71
+>=============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 0.00352669 0.337495 0.0932776 0.210122 0.355579 9999 20
+2 0.0519495 0.00225598 0.350896 0.145345 0.218803 0.230751 9999 40
+3 0 0.00871272 0.562215 0.0364771 0.0874418 0.305154 9999 60
+4 0.0516033 0 0.176566 0.0144248 0.142869 0.614537 9999 80
+5 0.0702494 0 0.135112 0.0511727 0.132006 0.61146 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/cv2/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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>45050 DEG expressed across 6 samples were identified
+>Group size: 454, Kappa: 11.6692002390198
+>Best kappa: 11.6692002390198 
+>SVD UpperRightDiag: 58048.1
+>SVD LowerRightDiag: 4974.47
+>=============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 0.0453088 0 0.176577 0.0961616 0.135575 0.546377 9999 16.6667
+2 0.0930713 0 0.180161 0.0436568 0.155936 0.527175 9999 33.3333
+3 0.0582994 0 0.279106 0.0106818 0.158044 0.493869 9999 50
+4 0.0128597 0.0305292 0.274773 0 0.230628 0.451209 9999 66.6667
+5 0.0187485 0.0251728 0.149362 0.00254185 0.244765 0.55941 9999 83.3333
+6 0.0237898 0.0154267 0.261989 0 0.196697 0.502097 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ye2026_sepsis/fewshot4/out_hires/fractions_results.txt

@@ -0,0 +1,78 @@
+Mixture	B cell	DC	Monocyte	NK cell	Other	T cell
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+Abd-PS23	0.2440844266859768	0.0	0.1298014626697325	0.0	0.3667437543977953	0.2593703562464954
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+Abd-S66	0.1262557359533708	0.1190063394247263	0.3609091949560803	0.2115207000087829	0.0794065427770301	0.1029014868800093
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+HC09	0.0287140375558479	0.2219140946557238	0.0609430854777094	0.238079539891073	0.0	0.4503492424196458
+HC12	0.0192485440376372	0.1891302393699242	0.063037918494909	0.2878309472666535	0.0305106055830543	0.4102417452478214
+HC13	0.053053676250612	0.1745422233035841	0.0258502263685394	0.2780672641785494	0.023974593082712	0.4445120168160028
+HC16	0.0	0.1789289438577358	0.0	0.5325189839512565	0.0088641362614112	0.2796879359295963
+IC10	0.0771150460317963	0.105294489194174	0.0602584939847246	0.1479471574610988	0.117496386797387	0.4918884265308191
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+IC22	0.0	0.2839592281743576	0.358867608388023	0.064156798411167	0.0790431524889153	0.2139732125375368
+PHC01	0.1099602734082614	0.214240762724235	0.0	0.1045190985269273	0.0214814757669157	0.5497983895736603
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