__STDOUT LOG__ Job runs on fgcz-h-162 at /scratch/EdgeR_diff--over--undiff_2024-12-04--16-02-56_temp1336689 Starting EzAppEdger diff--over--undiff EdgeR_diff--over--undiff_2024-12-04--16-02-56_temp1336689 2024-12-04 16:03:03 ezRun tag: f6fc46b7fcb9978c7ad4a62b66f23ff47544350d ezRun github link: https://github.com/uzh/ezRun/tree/f6fc46b7fcb9978c7ad4a62b66f23ff47544350d R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 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: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] parallel tools stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] gplots_3.1.3.1 annotate_1.82.0 [3] XML_3.99-0.16.1 GOstats_2.70.0 [5] graph_1.82.0 Category_2.70.0 [7] pheatmap_1.0.12 RColorBrewer_1.1-3 [9] ggrepel_0.9.5 htmltools_0.5.8.1 [11] SingleCellExperiment_1.26.0 Matrix_1.7-0 [13] tidyselect_1.2.1 writexl_1.5.0 [15] DT_0.33 DOSE_3.30.1 [17] BiocParallel_1.38.0 readxl_1.4.3 [19] htmlwidgets_1.6.4 webshot_0.5.5 [21] plotly_4.10.4 kableExtra_1.4.0 [23] knitr_1.47 clusterProfiler_4.12.0 [25] GO.db_3.19.1 AnnotationDbi_1.66.0 [27] edgeR_4.2.0 limma_3.60.2 [29] rtracklayer_1.64.0 SummarizedExperiment_1.34.0 [31] Biobase_2.64.0 MatrixGenerics_1.16.0 [33] matrixStats_1.3.0 withr_3.0.0 [35] ezRun_3.19.1 lubridate_1.9.3 [37] forcats_1.0.0 stringr_1.5.1 [39] dplyr_1.1.4 purrr_1.0.2 [41] readr_2.1.5 tidyr_1.3.1 [43] tibble_3.2.1 ggplot2_3.5.1 [45] tidyverse_2.0.0 GenomicRanges_1.56.1 [47] Biostrings_2.72.1 GenomeInfoDb_1.40.1 [49] XVector_0.44.0 IRanges_2.38.0 [51] S4Vectors_0.42.0 BiocGenerics_0.50.0 [53] data.table_1.15.4 loaded via a namespace (and not attached): [1] splines_4.4.0 BiocIO_1.14.0 filelock_1.0.3 [4] bitops_1.0-7 ggplotify_0.1.2 BiasedUrn_2.0.12 [7] cellranger_1.1.0 polyclip_1.10-6 httr2_1.0.1 [10] lifecycle_1.0.4 lattice_0.22-6 vroom_1.6.5 [13] MASS_7.3-61 crosstalk_1.2.1 magrittr_2.0.3 [16] openxlsx_4.2.5.2 sass_0.4.9 rmarkdown_2.27 [19] jquerylib_0.1.4 yaml_2.3.8 zip_2.3.1 [22] cowplot_1.1.3 DBI_1.2.3 abind_1.4-5 [25] zlibbioc_1.50.0 ggraph_2.2.1 RCurl_1.98-1.14 [28] yulab.utils_0.1.4 rappdirs_0.3.3 tweenr_2.0.3 [31] GenomeInfoDbData_1.2.12 enrichplot_1.24.0 AnnotationForge_1.46.0 [34] tidytree_0.4.6 genefilter_1.86.0 svglite_2.1.3 [37] codetools_0.2-20 DelayedArray_0.30.1 xml2_1.3.6 [40] ggforce_0.4.2 aplot_0.2.3 UCSC.utils_1.0.0 [43] farver_2.1.2 goseq_1.56.0 viridis_0.6.5 [46] BiocFileCache_2.12.0 GenomicAlignments_1.40.0 jsonlite_1.8.8 [49] tidygraph_1.3.1 ggridges_0.5.6 survival_3.7-0 [52] systemfonts_1.1.0 ggnewscale_0.4.10 progress_1.2.3 [55] treeio_1.28.0 Rcpp_1.0.12 glue_1.7.0 [58] gridExtra_2.3 SparseArray_1.4.8 geneLenDataBase_1.40.1 [61] mgcv_1.9-1 xfun_0.45 qvalue_2.36.0 [64] fastmap_1.2.0 fansi_1.0.6 caTools_1.18.2 [67] digest_0.6.35 timechange_0.3.0 R6_2.5.1 [70] gridGraphics_0.5-1 colorspace_2.1-1 gtools_3.9.5 [73] biomaRt_2.60.0 RSQLite_2.3.7 utf8_1.2.4 [76] generics_0.1.3 prettyunits_1.2.0 graphlayouts_1.1.1 [79] httr_1.4.7 S4Arrays_1.4.1 scatterpie_0.2.3 [82] pkgconfig_2.0.3 gtable_0.3.5 blob_1.2.4 [85] shadowtext_0.1.3 fgsea_1.30.0 RBGL_1.80.0 [88] GSEABase_1.66.0 scales_1.3.0 png_0.1-8 [91] ggfun_0.1.5 rstudioapi_0.16.0 tzdb_0.4.0 [94] reshape2_1.4.4 rjson_0.2.21 nlme_3.1-165 [97] curl_5.2.1 cachem_1.1.0 KernSmooth_2.23-24 [100] HDO.db_0.99.1 restfulr_0.0.15 pillar_1.9.0 [103] grid_4.4.0 vctrs_0.6.5 dbplyr_2.5.0 [106] xtable_1.8-4 Rgraphviz_2.48.0 evaluate_0.24.0 [109] GenomicFeatures_1.56.0 cli_3.6.2 locfit_1.5-9.9 [112] compiler_4.4.0 Rsamtools_2.20.0 rlang_1.1.4 [115] crayon_1.5.2 labeling_0.4.3 plyr_1.8.9 [118] fs_1.6.4 stringi_1.8.4 viridisLite_0.4.2 [121] txdbmaker_1.0.0 munsell_0.5.1 lazyeval_0.2.2 [124] GOSemSim_2.30.0 hms_1.1.3 patchwork_1.2.0 [127] bit64_4.0.5 KEGGREST_1.44.0 statmod_1.5.0 [130] highr_0.11 igraph_2.0.3 memoise_2.0.1 [133] bslib_0.7.0 ggtree_3.12.0 fastmatch_1.1-4 [136] bit_4.0.5 ape_5.8 gson_0.1.0 Finished EzAppEdger diff--over--undiff EdgeR_diff--over--undiff_2024-12-04--16-02-56_temp1336689 2024-12-04 16:10:02 [1] "Success" __SCRIPT END__ __STDERR LOG__ Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.1 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.1 ✔ purrr 1.0.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors unknown param: partition unknown param: sampleGroupBaseline unknown param: refGroupBaseline unknown param: Rversion unknown param: sushi_app unknown param: isLastJob Loading required package: withr Loading required package: tools Attaching package: ‘tools’ The following object is masked from ‘package:withr’: makevars_user Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S1_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S2_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S3_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S4_diff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S5_diff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p6015/FeatureCounts_2024-12-04--15-21-31/S6_diff.txt Loading required package: rtracklayer Using gene level annotation: /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30/Genes/genes_annotation_byGene.txt 2024-12-04--16-03-12 twoGroupCountComparison start Loading required package: edgeR Loading required package: limma Attaching package: ‘limma’ The following object is masked from ‘package:ezRun’: trimWhiteSpace The following object is masked from ‘package:BiocGenerics’: plotMA Using quasi-likelihood (QL) F-test! 2024-12-04--16-03-16 twoGroupCountComparison done: 0.06745 min doGo: TRUE Loading required package: GO.db Loading required package: AnnotationDbi Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:dplyr’: select Loading required package: clusterProfiler clusterProfiler v4.12.0 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/ If you use clusterProfiler in published research, please cite: T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141 Attaching package: ‘clusterProfiler’ The following object is masked from ‘package:AnnotationDbi’: select The following object is masked from ‘package:purrr’: simplify The following object is masked from ‘package:XVector’: slice The following object is masked from ‘package:IRanges’: slice The following object is masked from ‘package:S4Vectors’: rename The following object is masked from ‘package:stats’: filter Loading required package: parallel using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections... GSEA analysis... leading edge analysis... done... using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections... GSEA analysis... leading edge analysis... done... using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019). preparing geneSet collections... GSEA analysis... leading edge analysis... done... There were 16 warnings (use warnings() to see them)