Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cibersortx_test_20261006T232059.log

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+2026-10-06T23:20:59 lane test: 4 cores, steps fractions,hires, cohorts ye2026_sepsis
+2026-10-06T23:20:59 --- fractions ye2026_sepsis fewshot0
+2026-10-07T00:00:54 fractions ye2026_sepsis fewshot0: 2395 s
+2026-10-07T00:00:54 --- hires ye2026_sepsis fewshot0
+2026-10-07T11:54:29 WARN: hires ye2026_sepsis fewshot0 failed (logs/cx_hires_ye2026_sepsis_fewshot0.log)
+2026-10-07T11:54:29 lane test finished; failed=1

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_cv0.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 18280 rows
+>=============Make Signature Matrix=============
+>Maximum condition number (kappa):999
+>45880 DEG expressed across 6 samples were identified
+>Group size: 461, Kappa: 10.6403333978182
+>Best kappa: 10.6403333978182 
+>SVD UpperRightDiag: 60232.3
+>SVD LowerRightDiag: 5660.76
+>=============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 0.598677 0.0661387 0.176319 0.158866 9999 25
+2 0.00893464 0.0272707 0.336243 0.124785 0.326671 0.176096 9999 50
+3 0.0196307 0.00442816 0.0975212 0.0400705 0.122189 0.71616 9999 75
+4 0.060647 0 0.149781 0.00691218 0.0936601 0.689 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/logs/cx_fractions_giroux2022_cv1.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 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/logs/cx_fractions_giroux2022_cv2.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 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