=== Log started: 2026-03-05 00:56:15.694146 === Session info: R version 4.5.2 (2025-10-31) Platform: x86_64-conda-linux-gnu Running under: Ubuntu 24.04.4 LTS Matrix products: default BLAS/LAPACK: /home/shared/8TB_HDD_02/shedurkin/.local/share/r-miniconda/envs/r_enet_rscript/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/Los_Angeles tzcode source: system (glibc) attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pbapply_1.7-4 doParallel_1.0.17 [3] iterators_1.0.14 foreach_1.5.2 [5] scales_1.4.0 genefilter_1.80.3 [7] ggfortify_0.4.18 vegan_2.7-1 [9] permute_0.9-8 factoextra_1.0.7 [11] caret_7.0-1 lattice_0.22-7 [13] glmnet_4.1-10 Matrix_1.7-4 [15] pheatmap_1.0.13 rvest_1.0.5 [17] corrplot_0.95 ggcorrplot_0.1.4.1 [19] reshape2_1.4.4 edgeR_3.40.2 [21] limma_3.54.2 WGCNA_1.73 [23] fastcluster_1.3.0 dynamicTreeCut_1.63-1 [25] ggraph_2.2.1 tidygraph_1.3.1 [27] psych_2.5.6 igraph_2.1.4 [29] DESeq2_1.38.3 SummarizedExperiment_1.28.0 [31] Biobase_2.58.0 MatrixGenerics_1.10.0 [33] matrixStats_1.5.0 GenomicRanges_1.50.2 [35] GenomeInfoDb_1.34.9 IRanges_2.32.0 [37] S4Vectors_0.36.2 BiocGenerics_0.44.0 [39] lubridate_1.9.4 forcats_1.0.1 [41] stringr_1.6.0 dplyr_1.1.4 [43] purrr_1.2.0 readr_2.1.6 [45] tidyr_1.3.1 tibble_3.3.0 [47] ggplot2_3.5.2 tidyverse_2.0.0 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 shape_1.4.6.1 rstudioapi_0.17.1 [4] magrittr_2.0.4 farver_2.1.2 rmarkdown_2.29 [7] zlibbioc_1.44.0 vctrs_0.6.5 memoise_2.0.1 [10] RCurl_1.98-1.17 base64enc_0.1-3 htmltools_0.5.8.1 [13] pROC_1.18.5 Formula_1.2-5 parallelly_1.45.0 [16] htmlwidgets_1.6.4 plyr_1.8.9 impute_1.72.3 [19] cachem_1.1.0 lifecycle_1.0.4 pkgconfig_2.0.3 [22] R6_2.6.1 fastmap_1.2.0 future_1.58.0 [25] GenomeInfoDbData_1.2.9 digest_0.6.39 colorspace_2.1-2 [28] AnnotationDbi_1.60.2 geneplotter_1.76.0 Hmisc_5.2-3 [31] RSQLite_2.4.2 timechange_0.3.0 mgcv_1.9-4 [34] httr_1.4.7 polyclip_1.10-7 compiler_4.5.2 [37] bit64_4.6.0-1 withr_3.0.2 htmlTable_2.4.3 [40] backports_1.5.0 BiocParallel_1.32.6 viridis_0.6.5 [43] DBI_1.2.3 ggforce_0.5.0 lava_1.8.1 [46] MASS_7.3-65 DelayedArray_0.24.0 ModelMetrics_1.2.2.2 [49] tools_4.5.2 foreign_0.8-90 future.apply_1.20.0 [52] nnet_7.3-20 glue_1.8.0 nlme_3.1-168 [55] grid_4.5.2 checkmate_2.3.2 cluster_2.1.8.1 [58] recipes_1.3.1 generics_0.1.4 gtable_0.3.6 [61] tzdb_0.5.0 class_7.3-23 preprocessCore_1.60.2 [64] data.table_1.17.8 hms_1.1.4 xml2_1.5.0 [67] XVector_0.38.0 ggrepel_0.9.6 pillar_1.11.1 [70] splines_4.5.2 tweenr_2.0.3 survival_3.8-3 [73] bit_4.6.0 annotate_1.76.0 tidyselect_1.2.1 [76] GO.db_3.16.0 locfit_1.5-9.12 Biostrings_2.66.0 [79] knitr_1.50 gridExtra_2.3 xfun_0.54 [82] graphlayouts_1.2.2 hardhat_1.4.1 timeDate_4041.110 [85] stringi_1.8.7 evaluate_1.0.5 codetools_0.2-20 [88] cli_3.6.5 rpart_4.1.24 xtable_1.8-4 [91] dichromat_2.0-0.1 Rcpp_1.1.0 globals_0.18.0 [94] png_0.1-8 XML_3.99-0.18 gower_1.0.2 [97] blob_1.2.4 bitops_1.0-9 listenv_0.9.1 [100] viridisLite_0.4.2 ipred_0.9-15 prodlim_2025.04.28 [103] crayon_1.5.3 rlang_1.1.6 KEGGREST_1.38.0 [106] mnormt_2.1.1 Start time:2026-03-05 00:56:15.737421 Defining model functions Loading gene counts Loading miRNA counts Loading lncRNA counts Loading WGBS data Loading metadata table Species prefix and code:POR,Peve WGBS column name handling Filtering datasets filtering low count features Ensuring integer counts Filtered dimensions: Genes: 471 x 31 miRNA: 46 x 31 lncRNA: 8317 x 31 WGBS: 19570 x 31 Ensuring all dfs have identical column names and orders Applying variance stabilization Predictor set dimensions:31 Predictor set dimensions:27933 Gene set dimensions:31 Gene set dimensions:471 === Data Validation and Cleaning === Predictor matrix: 31 samples x 27933 features Columns with NaN: 0 Columns with Inf: 0 Columns with NA: 9498 Constant columns (sd = 0): 0 Total problematic columns: 9498 Problematic columns by type: Other: 9498 Removed 9498 problematic predictors. Remaining: 18435 Response matrix: 31 samples x 471 genes Genes with NaN/Inf/NA/constant values: 0 Samples available: 31 Cleaned data dimensions: Predictors: 31 samples x 18435 features Genes: 31 samples x 471 genes Pre-flight test: fitting one gene sequentially to verify data compatibility... Pre-flight passed: gene 'OG_08920', R2 = 0.9997, 109 non-zero coefficients === Data validation complete === === PART 1: Elastic Net with Bootstrapped Train/Test Splits === --- Round 1: 10 bootstrap replicates across all 471 genes --- Round1: Running 10 replicates across 10 cores... Round1: 0/10 (0.0%) Round1: 10/10 (100.0%) Round 1 results: 195/471 genes with mean R2 >= 0.50 --- Round 2: 10 bootstrap replicates on 195 well-predicted genes --- Round2: Running 10 replicates across 10 cores... Round2: 0/10 (0.0%) Round2: 10/10 (100.0%) Round 2 performance summary: Min. 1st Qu. Median Mean 3rd Qu. Max. 0.1818 0.5657 0.6604 0.6667 0.7749 0.9407 Bootstrapping completed in 12.01 minutes === PART 1.5: R-squared Bootstrap Plots === Plotting Round 1 R² (all genes)... Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_R2_round1-allgenes.png Plotting Round 2 R² (well-predicted genes)... Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_R2_round2-well-predictedgenes.png === PART 2: Stability Selection for Predictor Reliability === This step assesses how reliably each predictor is selected across random subsamples of the data, providing a robust measure of predictor importance. Unlike permutation testing, stability selection avoids the degenerate null distribution problem that arises with sparse penalized regression. Running stability selection for 195 well-predicted genes Calculating stability selection for 195 genes with 200 subsample iterations each Total predictors per gene: 18435 Using 10 core(s) for gene-level parallelization Complementary pairs: each iteration produces 2 fits (400 total fits per gene) StabSel: Running in parallel mode across 195 genes... StabSel: 0/195 (0.0%) StabSel: 195/195 (100.0%) === Stability Selection Summary === Total predictor-gene combinations: 3594825 Predictors ever selected (in at least 1 fit): 280837 (7.81%) Average predictors with any selection per gene: 1440.2 Subsample iterations per gene: 200 (producing 400 complementary-pair fits) Stability selection completed in 130.47 minutes Applying PFER bound with selection threshold pi = 0.60 PFER bound applied with selection threshold pi = 0.60 Theoretical guarantee: E(false selections) <= PFER_bound per gene Per-gene PFER diagnostics: OG_00246: PFER <= 1.860 | Stable predictors: 23 | Avg selected/fit: 82.8 | p = 18435 OG_00355: PFER <= 2.676 | Stable predictors: 27 | Avg selected/fit: 99.3 | p = 18435 OG_00430: PFER <= 2.215 | Stable predictors: 36 | Avg selected/fit: 90.4 | p = 18435 OG_00460: PFER <= 1.308 | Stable predictors: 16 | Avg selected/fit: 69.4 | p = 18435 OG_00514: PFER <= 2.171 | Stable predictors: 20 | Avg selected/fit: 89.5 | p = 18435 OG_00572: PFER <= 2.750 | Stable predictors: 43 | Avg selected/fit: 100.7 | p = 18435 OG_00807: PFER <= 3.001 | Stable predictors: 56 | Avg selected/fit: 105.2 | p = 18435 OG_00843: PFER <= 2.415 | Stable predictors: 30 | Avg selected/fit: 94.4 | p = 18435 OG_01023: PFER <= 2.548 | Stable predictors: 19 | Avg selected/fit: 96.9 | p = 18435 OG_01117: PFER <= 2.548 | Stable predictors: 38 | Avg selected/fit: 96.9 | p = 18435 OG_01121: PFER <= 2.388 | Stable predictors: 37 | Avg selected/fit: 93.8 | p = 18435 OG_01155: PFER <= 2.916 | Stable predictors: 34 | Avg selected/fit: 103.7 | p = 18435 OG_01177: PFER <= 1.824 | Stable predictors: 26 | Avg selected/fit: 82.0 | p = 18435 OG_01317: PFER <= 2.407 | Stable predictors: 27 | Avg selected/fit: 94.2 | p = 18435 OG_01353: PFER <= 2.648 | Stable predictors: 32 | Avg selected/fit: 98.8 | p = 18435 OG_01354: PFER <= 2.644 | Stable predictors: 44 | Avg selected/fit: 98.7 | p = 18435 OG_01486: PFER <= 3.041 | Stable predictors: 52 | Avg selected/fit: 105.9 | p = 18435 OG_01489: PFER <= 2.648 | Stable predictors: 21 | Avg selected/fit: 98.8 | p = 18435 OG_01579: PFER <= 2.066 | Stable predictors: 19 | Avg selected/fit: 87.3 | p = 18435 OG_01608: PFER <= 2.765 | Stable predictors: 37 | Avg selected/fit: 101.0 | p = 18435 OG_01611: PFER <= 2.626 | Stable predictors: 28 | Avg selected/fit: 98.4 | p = 18435 OG_01630: PFER <= 2.337 | Stable predictors: 38 | Avg selected/fit: 92.8 | p = 18435 OG_01727: PFER <= 3.074 | Stable predictors: 53 | Avg selected/fit: 106.5 | p = 18435 OG_01747: PFER <= 2.110 | Stable predictors: 26 | Avg selected/fit: 88.2 | p = 18435 OG_01999: PFER <= 2.031 | Stable predictors: 25 | Avg selected/fit: 86.5 | p = 18435 OG_02000: PFER <= 1.787 | Stable predictors: 40 | Avg selected/fit: 81.2 | p = 18435 OG_02012: PFER <= 3.210 | Stable predictors: 33 | Avg selected/fit: 108.8 | p = 18435 OG_02090: PFER <= 2.292 | Stable predictors: 43 | Avg selected/fit: 91.9 | p = 18435 OG_02102: PFER <= 2.545 | Stable predictors: 36 | Avg selected/fit: 96.9 | p = 18435 OG_02124: PFER <= 2.576 | Stable predictors: 24 | Avg selected/fit: 97.5 | p = 18435 OG_02149: PFER <= 2.082 | Stable predictors: 16 | Avg selected/fit: 87.6 | p = 18435 OG_02184: PFER <= 2.777 | Stable predictors: 34 | Avg selected/fit: 101.2 | p = 18435 OG_02190: PFER <= 3.009 | Stable predictors: 44 | Avg selected/fit: 105.3 | p = 18435 OG_02219: PFER <= 2.281 | Stable predictors: 22 | Avg selected/fit: 91.7 | p = 18435 OG_02220: PFER <= 2.154 | Stable predictors: 23 | Avg selected/fit: 89.1 | p = 18435 OG_02260: PFER <= 1.909 | Stable predictors: 24 | Avg selected/fit: 83.9 | p = 18435 OG_02358: PFER <= 2.348 | Stable predictors: 31 | Avg selected/fit: 93.1 | p = 18435 OG_03267: PFER <= 2.759 | Stable predictors: 28 | Avg selected/fit: 100.9 | p = 18435 OG_03298: PFER <= 2.372 | Stable predictors: 25 | Avg selected/fit: 93.5 | p = 18435 OG_03330: PFER <= 2.263 | Stable predictors: 29 | Avg selected/fit: 91.3 | p = 18435 OG_03628: PFER <= 1.983 | Stable predictors: 21 | Avg selected/fit: 85.5 | p = 18435 OG_03780: PFER <= 1.712 | Stable predictors: 24 | Avg selected/fit: 79.4 | p = 18435 OG_03850: PFER <= 1.606 | Stable predictors: 20 | Avg selected/fit: 76.9 | p = 18435 OG_04209: PFER <= 2.386 | Stable predictors: 38 | Avg selected/fit: 93.8 | p = 18435 OG_04238: PFER <= 2.176 | Stable predictors: 52 | Avg selected/fit: 89.6 | p = 18435 OG_04243: PFER <= 2.334 | Stable predictors: 26 | Avg selected/fit: 92.8 | p = 18435 OG_04247: PFER <= 1.015 | Stable predictors: 17 | Avg selected/fit: 61.2 | p = 18435 OG_04327: PFER <= 2.288 | Stable predictors: 26 | Avg selected/fit: 91.8 | p = 18435 OG_04538: PFER <= 1.964 | Stable predictors: 28 | Avg selected/fit: 85.1 | p = 18435 OG_04547: PFER <= 2.565 | Stable predictors: 38 | Avg selected/fit: 97.2 | p = 18435 OG_04560: PFER <= 1.855 | Stable predictors: 39 | Avg selected/fit: 82.7 | p = 18435 OG_04723: PFER <= 2.249 | Stable predictors: 27 | Avg selected/fit: 91.1 | p = 18435 OG_04756: PFER <= 2.390 | Stable predictors: 23 | Avg selected/fit: 93.9 | p = 18435 OG_04789: PFER <= 1.842 | Stable predictors: 18 | Avg selected/fit: 82.4 | p = 18435 OG_04799: PFER <= 3.358 | Stable predictors: 54 | Avg selected/fit: 111.3 | p = 18435 OG_05121: PFER <= 1.932 | Stable predictors: 26 | Avg selected/fit: 84.4 | p = 18435 OG_05308: PFER <= 2.509 | Stable predictors: 24 | Avg selected/fit: 96.2 | p = 18435 OG_05366: PFER <= 2.278 | Stable predictors: 30 | Avg selected/fit: 91.6 | p = 18435 OG_05367: PFER <= 2.181 | Stable predictors: 31 | Avg selected/fit: 89.7 | p = 18435 OG_05498: PFER <= 2.384 | Stable predictors: 26 | Avg selected/fit: 93.7 | p = 18435 OG_05514: PFER <= 2.136 | Stable predictors: 23 | Avg selected/fit: 88.7 | p = 18435 OG_05637: PFER <= 2.756 | Stable predictors: 28 | Avg selected/fit: 100.8 | p = 18435 OG_05713: PFER <= 2.450 | Stable predictors: 29 | Avg selected/fit: 95.1 | p = 18435 OG_05718: PFER <= 2.592 | Stable predictors: 45 | Avg selected/fit: 97.8 | p = 18435 OG_05749: PFER <= 2.004 | Stable predictors: 26 | Avg selected/fit: 86.0 | p = 18435 OG_05856: PFER <= 2.447 | Stable predictors: 30 | Avg selected/fit: 95.0 | p = 18435 OG_05874: PFER <= 1.889 | Stable predictors: 36 | Avg selected/fit: 83.4 | p = 18435 OG_05875: PFER <= 1.790 | Stable predictors: 33 | Avg selected/fit: 81.2 | p = 18435 OG_06152: PFER <= 2.639 | Stable predictors: 33 | Avg selected/fit: 98.6 | p = 18435 OG_06181: PFER <= 2.419 | Stable predictors: 31 | Avg selected/fit: 94.4 | p = 18435 OG_06198: PFER <= 2.307 | Stable predictors: 34 | Avg selected/fit: 92.2 | p = 18435 OG_06279: PFER <= 2.084 | Stable predictors: 37 | Avg selected/fit: 87.7 | p = 18435 OG_06599: PFER <= 2.722 | Stable predictors: 38 | Avg selected/fit: 100.2 | p = 18435 OG_06607: PFER <= 2.235 | Stable predictors: 33 | Avg selected/fit: 90.8 | p = 18435 OG_06616: PFER <= 2.225 | Stable predictors: 28 | Avg selected/fit: 90.6 | p = 18435 OG_06670: PFER <= 2.500 | Stable predictors: 17 | Avg selected/fit: 96.0 | p = 18435 OG_06717: PFER <= 1.943 | Stable predictors: 26 | Avg selected/fit: 84.6 | p = 18435 OG_06719: PFER <= 2.041 | Stable predictors: 25 | Avg selected/fit: 86.7 | p = 18435 OG_06754: PFER <= 2.312 | Stable predictors: 24 | Avg selected/fit: 92.3 | p = 18435 OG_06998: PFER <= 2.811 | Stable predictors: 38 | Avg selected/fit: 101.8 | p = 18435 OG_07000: PFER <= 1.849 | Stable predictors: 27 | Avg selected/fit: 82.6 | p = 18435 OG_07183: PFER <= 2.143 | Stable predictors: 21 | Avg selected/fit: 88.9 | p = 18435 OG_07252: PFER <= 1.425 | Stable predictors: 12 | Avg selected/fit: 72.5 | p = 18435 OG_07331: PFER <= 3.113 | Stable predictors: 42 | Avg selected/fit: 107.1 | p = 18435 OG_07389: PFER <= 1.561 | Stable predictors: 19 | Avg selected/fit: 75.9 | p = 18435 OG_07620: PFER <= 1.649 | Stable predictors: 24 | Avg selected/fit: 78.0 | p = 18435 OG_07641: PFER <= 2.098 | Stable predictors: 25 | Avg selected/fit: 87.9 | p = 18435 OG_07807: PFER <= 2.103 | Stable predictors: 22 | Avg selected/fit: 88.0 | p = 18435 OG_07892: PFER <= 2.088 | Stable predictors: 39 | Avg selected/fit: 87.7 | p = 18435 OG_07958: PFER <= 2.006 | Stable predictors: 18 | Avg selected/fit: 86.0 | p = 18435 OG_08143: PFER <= 1.575 | Stable predictors: 16 | Avg selected/fit: 76.2 | p = 18435 OG_08144: PFER <= 1.583 | Stable predictors: 24 | Avg selected/fit: 76.4 | p = 18435 OG_08347: PFER <= 2.552 | Stable predictors: 37 | Avg selected/fit: 97.0 | p = 18435 OG_08432: PFER <= 2.271 | Stable predictors: 35 | Avg selected/fit: 91.5 | p = 18435 OG_08497: PFER <= 2.184 | Stable predictors: 27 | Avg selected/fit: 89.7 | p = 18435 OG_08528: PFER <= 2.565 | Stable predictors: 29 | Avg selected/fit: 97.2 | p = 18435 OG_08622: PFER <= 2.347 | Stable predictors: 27 | Avg selected/fit: 93.0 | p = 18435 OG_08793: PFER <= 1.852 | Stable predictors: 18 | Avg selected/fit: 82.6 | p = 18435 OG_08842: PFER <= 1.633 | Stable predictors: 31 | Avg selected/fit: 77.6 | p = 18435 OG_08856: PFER <= 2.670 | Stable predictors: 31 | Avg selected/fit: 99.2 | p = 18435 OG_08920: PFER <= 2.666 | Stable predictors: 31 | Avg selected/fit: 99.2 | p = 18435 OG_09247: PFER <= 1.939 | Stable predictors: 23 | Avg selected/fit: 84.6 | p = 18435 OG_09310: PFER <= 2.813 | Stable predictors: 38 | Avg selected/fit: 101.8 | p = 18435 OG_09423: PFER <= 2.399 | Stable predictors: 33 | Avg selected/fit: 94.0 | p = 18435 OG_09597: PFER <= 2.231 | Stable predictors: 42 | Avg selected/fit: 90.7 | p = 18435 OG_09598: PFER <= 2.218 | Stable predictors: 24 | Avg selected/fit: 90.4 | p = 18435 OG_09806: PFER <= 1.956 | Stable predictors: 34 | Avg selected/fit: 84.9 | p = 18435 OG_09896: PFER <= 1.924 | Stable predictors: 29 | Avg selected/fit: 84.2 | p = 18435 OG_09969: PFER <= 1.980 | Stable predictors: 45 | Avg selected/fit: 85.4 | p = 18435 OG_10002: PFER <= 1.917 | Stable predictors: 42 | Avg selected/fit: 84.1 | p = 18435 OG_10007: PFER <= 2.307 | Stable predictors: 45 | Avg selected/fit: 92.2 | p = 18435 OG_10008: PFER <= 2.462 | Stable predictors: 50 | Avg selected/fit: 95.3 | p = 18435 OG_10121: PFER <= 2.720 | Stable predictors: 23 | Avg selected/fit: 100.1 | p = 18435 OG_10183: PFER <= 2.159 | Stable predictors: 50 | Avg selected/fit: 89.2 | p = 18435 OG_10205: PFER <= 1.994 | Stable predictors: 32 | Avg selected/fit: 85.7 | p = 18435 OG_10265: PFER <= 2.357 | Stable predictors: 11 | Avg selected/fit: 93.2 | p = 18435 OG_10332: PFER <= 1.792 | Stable predictors: 35 | Avg selected/fit: 81.3 | p = 18435 OG_10509: PFER <= 2.533 | Stable predictors: 42 | Avg selected/fit: 96.6 | p = 18435 OG_10516: PFER <= 1.779 | Stable predictors: 24 | Avg selected/fit: 81.0 | p = 18435 OG_10522: PFER <= 2.442 | Stable predictors: 18 | Avg selected/fit: 94.9 | p = 18435 OG_10675: PFER <= 2.691 | Stable predictors: 37 | Avg selected/fit: 99.6 | p = 18435 OG_10758: PFER <= 1.963 | Stable predictors: 21 | Avg selected/fit: 85.1 | p = 18435 OG_10759: PFER <= 1.962 | Stable predictors: 25 | Avg selected/fit: 85.1 | p = 18435 OG_10936: PFER <= 2.814 | Stable predictors: 28 | Avg selected/fit: 101.9 | p = 18435 OG_11038: PFER <= 1.771 | Stable predictors: 28 | Avg selected/fit: 80.8 | p = 18435 OG_11215: PFER <= 0.884 | Stable predictors: 19 | Avg selected/fit: 57.1 | p = 18435 OG_11245: PFER <= 2.475 | Stable predictors: 42 | Avg selected/fit: 95.5 | p = 18435 OG_11379: PFER <= 1.402 | Stable predictors: 19 | Avg selected/fit: 71.9 | p = 18435 OG_11429: PFER <= 1.051 | Stable predictors: 14 | Avg selected/fit: 62.3 | p = 18435 OG_11642: PFER <= 2.839 | Stable predictors: 29 | Avg selected/fit: 102.3 | p = 18435 OG_11813: PFER <= 2.370 | Stable predictors: 35 | Avg selected/fit: 93.5 | p = 18435 OG_11831: PFER <= 2.418 | Stable predictors: 25 | Avg selected/fit: 94.4 | p = 18435 OG_11957: PFER <= 2.286 | Stable predictors: 32 | Avg selected/fit: 91.8 | p = 18435 OG_11984: PFER <= 3.078 | Stable predictors: 39 | Avg selected/fit: 106.5 | p = 18435 OG_12031: PFER <= 2.072 | Stable predictors: 20 | Avg selected/fit: 87.4 | p = 18435 OG_12107: PFER <= 3.338 | Stable predictors: 48 | Avg selected/fit: 110.9 | p = 18435 OG_12108: PFER <= 1.985 | Stable predictors: 34 | Avg selected/fit: 85.5 | p = 18435 OG_12109: PFER <= 1.943 | Stable predictors: 29 | Avg selected/fit: 84.6 | p = 18435 OG_12162: PFER <= 1.954 | Stable predictors: 25 | Avg selected/fit: 84.9 | p = 18435 OG_12165: PFER <= 3.079 | Stable predictors: 32 | Avg selected/fit: 106.6 | p = 18435 OG_12166: PFER <= 2.151 | Stable predictors: 44 | Avg selected/fit: 89.1 | p = 18435 OG_12242: PFER <= 1.907 | Stable predictors: 29 | Avg selected/fit: 83.8 | p = 18435 OG_12248: PFER <= 1.561 | Stable predictors: 14 | Avg selected/fit: 75.9 | p = 18435 OG_12318: PFER <= 1.941 | Stable predictors: 25 | Avg selected/fit: 84.6 | p = 18435 OG_12331: PFER <= 3.472 | Stable predictors: 53 | Avg selected/fit: 113.1 | p = 18435 OG_12424: PFER <= 1.930 | Stable predictors: 22 | Avg selected/fit: 84.3 | p = 18435 OG_12447: PFER <= 2.823 | Stable predictors: 31 | Avg selected/fit: 102.0 | p = 18435 OG_12496: PFER <= 2.585 | Stable predictors: 34 | Avg selected/fit: 97.6 | p = 18435 OG_12518: PFER <= 2.295 | Stable predictors: 39 | Avg selected/fit: 92.0 | p = 18435 OG_12568: PFER <= 1.873 | Stable predictors: 41 | Avg selected/fit: 83.1 | p = 18435 OG_12722: PFER <= 1.455 | Stable predictors: 14 | Avg selected/fit: 73.2 | p = 18435 OG_12785: PFER <= 1.837 | Stable predictors: 26 | Avg selected/fit: 82.3 | p = 18435 OG_12880: PFER <= 2.028 | Stable predictors: 31 | Avg selected/fit: 86.5 | p = 18435 OG_13013: PFER <= 2.670 | Stable predictors: 31 | Avg selected/fit: 99.2 | p = 18435 OG_13016: PFER <= 2.537 | Stable predictors: 39 | Avg selected/fit: 96.7 | p = 18435 OG_13050: PFER <= 1.424 | Stable predictors: 17 | Avg selected/fit: 72.5 | p = 18435 OG_13066: PFER <= 2.171 | Stable predictors: 31 | Avg selected/fit: 89.5 | p = 18435 OG_13197: PFER <= 2.451 | Stable predictors: 36 | Avg selected/fit: 95.1 | p = 18435 OG_13201: PFER <= 2.336 | Stable predictors: 42 | Avg selected/fit: 92.8 | p = 18435 OG_13239: PFER <= 2.489 | Stable predictors: 43 | Avg selected/fit: 95.8 | p = 18435 OG_13334: PFER <= 2.496 | Stable predictors: 36 | Avg selected/fit: 95.9 | p = 18435 OG_13428: PFER <= 1.534 | Stable predictors: 26 | Avg selected/fit: 75.2 | p = 18435 OG_13451: PFER <= 2.274 | Stable predictors: 25 | Avg selected/fit: 91.6 | p = 18435 OG_13466: PFER <= 2.263 | Stable predictors: 37 | Avg selected/fit: 91.3 | p = 18435 OG_13481: PFER <= 2.588 | Stable predictors: 39 | Avg selected/fit: 97.7 | p = 18435 OG_13484: PFER <= 2.243 | Stable predictors: 39 | Avg selected/fit: 90.9 | p = 18435 OG_15738: PFER <= 2.236 | Stable predictors: 27 | Avg selected/fit: 90.8 | p = 18435 OG_15796: PFER <= 2.000 | Stable predictors: 26 | Avg selected/fit: 85.9 | p = 18435 OG_15816: PFER <= 2.193 | Stable predictors: 19 | Avg selected/fit: 89.9 | p = 18435 OG_15877: PFER <= 2.168 | Stable predictors: 26 | Avg selected/fit: 89.4 | p = 18435 OG_16000: PFER <= 2.033 | Stable predictors: 15 | Avg selected/fit: 86.6 | p = 18435 OG_16145: PFER <= 1.693 | Stable predictors: 23 | Avg selected/fit: 79.0 | p = 18435 OG_16159: PFER <= 1.764 | Stable predictors: 24 | Avg selected/fit: 80.6 | p = 18435 OG_16192: PFER <= 2.248 | Stable predictors: 28 | Avg selected/fit: 91.0 | p = 18435 OG_16380: PFER <= 2.191 | Stable predictors: 28 | Avg selected/fit: 89.9 | p = 18435 OG_16489: PFER <= 2.531 | Stable predictors: 35 | Avg selected/fit: 96.6 | p = 18435 OG_16592: PFER <= 2.286 | Stable predictors: 30 | Avg selected/fit: 91.8 | p = 18435 OG_16654: PFER <= 1.814 | Stable predictors: 30 | Avg selected/fit: 81.8 | p = 18435 OG_16665: PFER <= 1.962 | Stable predictors: 30 | Avg selected/fit: 85.0 | p = 18435 OG_16747: PFER <= 1.399 | Stable predictors: 14 | Avg selected/fit: 71.8 | p = 18435 OG_16856: PFER <= 1.067 | Stable predictors: 17 | Avg selected/fit: 62.7 | p = 18435 OG_16944: PFER <= 2.939 | Stable predictors: 31 | Avg selected/fit: 104.1 | p = 18435 OG_16980: PFER <= 1.701 | Stable predictors: 31 | Avg selected/fit: 79.2 | p = 18435 OG_17058: PFER <= 2.819 | Stable predictors: 28 | Avg selected/fit: 101.9 | p = 18435 OG_17106: PFER <= 2.735 | Stable predictors: 34 | Avg selected/fit: 100.4 | p = 18435 OG_17176: PFER <= 1.423 | Stable predictors: 17 | Avg selected/fit: 72.4 | p = 18435 OG_17479: PFER <= 1.800 | Stable predictors: 21 | Avg selected/fit: 81.5 | p = 18435 OG_17483: PFER <= 1.957 | Stable predictors: 29 | Avg selected/fit: 84.9 | p = 18435 OG_17556: PFER <= 2.254 | Stable predictors: 29 | Avg selected/fit: 91.2 | p = 18435 OG_17666: PFER <= 1.770 | Stable predictors: 27 | Avg selected/fit: 80.8 | p = 18435 OG_17751: PFER <= 2.013 | Stable predictors: 31 | Avg selected/fit: 86.2 | p = 18435 OG_17800: PFER <= 1.433 | Stable predictors: 22 | Avg selected/fit: 72.7 | p = 18435 OG_17961: PFER <= 2.361 | Stable predictors: 28 | Avg selected/fit: 93.3 | p = 18435 OG_18057: PFER <= 1.796 | Stable predictors: 25 | Avg selected/fit: 81.4 | p = 18435 OG_18285: PFER <= 2.045 | Stable predictors: 24 | Avg selected/fit: 86.8 | p = 18435 === Stable Predictor Summary (Selection Prob >= 60%) === Number of stable predictor-gene associations: 5830 Number of genes with at least one stable predictor: 195 Breakdown of EVER-SELECTED predictors by type: # A tibble: 3 × 4 Predictor_Type N_ever_selected N_stable Pct_stable 1 Other 111597 574 0.514 2 lncRNA 168211 5249 3.12 3 miRNA 1029 7 0.680 Breakdown of STABLE predictors by type: # A tibble: 3 × 5 Predictor_Type N_stable N_unique_predictors N_genes_affected 1 Other 574 511 145 2 lncRNA 5249 3057 195 3 miRNA 7 6 7 # ℹ 1 more variable: Mean_Selection_Prob === PART 3: Generating Visualizations and Output Files === Creating summary plots... Creating per-gene stability selection plots... Saving stability selection results... Enhancing top predictors table with stability information... === PART 3.5: Stacked Bar Charts and Heatmaps === Building composition data (with significance filtering)... Building composition data (without significance filtering)... Generating stacked bar charts (stable predictors only)... Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_alphabetical_sig.png Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_predominant_sig.png Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_r2_sig.png Generating stacked bar charts (all non-zero predictors)... Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_alphabetical_nosig.png Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_predominant_nosig.png Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_stacked_bar_r2_nosig.png Generating predictor-type heatmaps... Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_predictor_heatmap_sig.png Saved: ../output/26.6-ElasticNet-stability-selection-2/Peve/Peve_predictor_heatmap_nosig.png === ANALYSIS COMPLETE === End time:2026-03-05 03:30:49.300711 Timing summary: - Bootstrapping: 12.01 minutes - Stability selection: 130.47 minutes - Total runtime: 142.48 minutes Output files generated: 1. Peve_stabsel_results_full.csv - All predictor-gene selection probabilities 2. Peve_stable_predictors.csv - Stable associations only (>= 60%) 3. Peve_gene_summary.csv - Summary per gene 4. Peve_predictor_type_summary.csv - Summary by predictor type 5. Peve_top_predictors_with_stability.csv - Top predictors with stability info 6. Peve_R2_round1*.png - R² per gene with error bars (all genes) 7. Peve_R2_round2*.png - R² per gene with error bars (well-predicted) 8. Peve_stacked_bar_*.png - Predictor type composition (3 orderings x 2 versions) 9. Peve_predictor_heatmap_*.png - Predictor type heatmap (2 versions) 10. Various per-gene plots in ../output/26.6-ElasticNet-stability-selection-2/Peve/ Key statistics: - Total genes analyzed: 471 - Well-predicted genes (R2 > 0.50): 195 - Stable predictor-gene associations: 5830 - Bootstrap replicates: 10 (round 1), 10 (round 2) - Subsample iterations: 200 (producing 400 complementary-pair fits) - Selection threshold: 60% - Cores used: 10 Statistical notes: - Predictor reliability assessed via stability selection (Meinshausen & Bühlmann, 2010; Shah & Samworth, 2013) - Error control: PFER bound (expected false selections per gene) - Selection threshold: pi = 0.60 - No separate multiple testing correction needed (PFER bound is simultaneous) Log file saved to: ../output/26.6-ElasticNet-stability-selection-2/Peve/ElasticNet_stabsel_log_20260305_005615.txt === END OF SCRIPT === === Log closed: 2026-03-05 03:30:49.359375 ===