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/fewshot3/hires_run.log

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+>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 11 mixture samples, 5563 genes, and 6 cell subsets...
+>Window size adaptively set to 7
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 162

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot3/out_fractions/.run.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
+>44153 DEG expressed across 6 samples were identified
+>Group size: 481, Kappa: 12.8671053188237
+>Best kappa: 12.8671053188237 
+>SVD UpperRightDiag: 60342
+>SVD LowerRightDiag: 4689.64
+>=============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 0.0291666 0.382535 0 0.219005 0.369293 9999 9.09091
+2 0.071216 0.00703171 0.448271 0.0485397 0.240293 0.184649 9999 18.1818
+3 0.113274 0 0.180008 0.147048 0.0763939 0.483276 9999 27.2727
+4 0.116071 0 0.162946 0.09386 0.143466 0.483656 9999 36.3636
+5 0.0548955 0.0197915 0.255246 0.0361238 0.142322 0.491622 9999 45.4545
+6 0.135094 0.026716 0.301306 0.0431026 0.227993 0.265789 9999 54.5455
+7 0.0179547 0.0244397 0.218918 0.0177332 0.295549 0.425405 9999 63.6364
+8 0.0329373 0.0377795 0.253217 0 0.206061 0.470005 9999 72.7273
+9 0 0 0.69544 0 0.0956875 0.208873 9999 81.8182
+10 0.0645813 0.0117557 0.188951 0 0.119508 0.615204 9999 90.9091
+11 0.0914625 0.00900582 0.164691 0 0.113844 0.620996 9999 100

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot4/hires_run.log

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+>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 10 mixture samples, 5563 genes, and 6 cell subsets...
+>Window size adaptively set to 7
+>Imputing high-resolution cell type GEPs...done.
+>Writing output to disk ...done.
+>Running time (sec): 107

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/giroux2022/fewshot4/out_fractions/.run.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
+>45593 DEG expressed across 6 samples were identified
+>Group size: 474, Kappa: 10.484106886885
+>Best kappa: 10.484106886885 
+>SVD UpperRightDiag: 60128.4
+>SVD LowerRightDiag: 5735.19
+>=============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 0 0.60398 0.0748945 0.101548 0.219577 9999 10
+2 0.0160469 0.0734395 0.303738 0.116683 0.264135 0.225958 9999 20
+3 0.0285168 0.107624 0.603812 0.10871 0.0296611 0.121677 9999 30
+4 0.0462915 0.0769986 0.102295 0.191577 0.211655 0.371183 9999 40
+5 0.0441096 0.0400439 0.175352 0.185688 0.205578 0.349229 9999 50
+6 0.0131109 0.0513124 0.055267 0 0.109691 0.770618 9999 60
+7 0.0766422 0.0239907 0.140404 0.00048782 0.0521194 0.706356 9999 70
+8 0.0368341 0.036752 0.192858 0 0.231585 0.50197 9999 80
+9 0.0373293 0.0213613 0.114916 0.0400504 0.2151 0.571243 9999 90
+10 0.0411904 0.0359353 0.198823 0.0309644 0.1713 0.521787 9999 100