ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'load' ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.5 ✔ purrr 0.3.4 ✔ tibble 3.1.5 ✔ dplyr 1.0.7 ✔ tidyr 1.1.4 ✔ stringr 1.4.0 ✔ readr 2.0.2 ✔ forcats 0.5.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following objects are masked from ‘package:dplyr’: collapse, desc, slice The following object is masked from ‘package:purrr’: reduce Loading required package: GenomicRanges Loading required package: GenomeInfoDb 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 converting counts to integer mode seqname source feature start end score strand frame 1 ##gff-version 3 NA NA 2 1 FIG CDS 1 1368 . + 1 3 1 FIG CDS 1379 2479 . + 2 4 1 FIG CDS 2485 3567 . + 1 5 1 FIG CDS 3631 4776 . - 1 6 1 FIG CDS 4813 5616 . - 1 att 1 2 ID=fig|888828.229.peg.1;Name=Chromosomal replication initiator protein DnaA 3 ID=fig|888828.229.peg.2;Name=DNA polymerase III beta subunit (EC 2.7.7.7);Ontology_term=KEGG_ENZYME:2.7.7.7 4 ID=fig|888828.229.peg.3;Name=DNA recombination and repair protein RecF 5 ID=fig|888828.229.peg.4;Name=N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25);Ontology_term=KEGG_ENZYME:3.5.1.25 6 ID=fig|888828.229.peg.5;Name=Glucosamine-6-phosphate deaminase (EC 3.5.99.6);Ontology_term=KEGG_ENZYME:3.5.99.6 seqname source feature start end score strand frame 2 1 FIG CDS 138 1231 . + 1 3 1 FIG CDS 1489 2369 . + 2 4 1 FIG CDS 2593 3459 . + 1 5 1 FIG CDS 3746 4662 . - 1 6 1 FIG CDS 4893 5536 . - 1 7 1 FIG CDS 5793 6495 . - 2 att 2 ID=fig|888828.229.peg.1;Name=Chromosomal replication initiator protein DnaA 3 ID=fig|888828.229.peg.2;Name=DNA polymerase III beta subunit (EC 2.7.7.7);Ontology_term=KEGG_ENZYME:2.7.7.7 4 ID=fig|888828.229.peg.3;Name=DNA recombination and repair protein RecF 5 ID=fig|888828.229.peg.4;Name=N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25);Ontology_term=KEGG_ENZYME:3.5.1.25 6 ID=fig|888828.229.peg.5;Name=Glucosamine-6-phosphate deaminase (EC 3.5.99.6);Ontology_term=KEGG_ENZYME:3.5.99.6 7 ID=fig|888828.229.peg.6;Name=N-acetylneuraminate lyase (EC 4.1.3.3);Ontology_term=KEGG_ENZYME:4.1.3.3 [1] "Generating pseudo-datasets" Joining, by = "Pos" [1] 1 Joining, by = "Pos" [1] 2 Joining, by = "Pos" [1] 3 Joining, by = "Pos" [1] 4 Joining, by = "Pos" [1] 5 Joining, by = "Pos" [1] 6 Joining, by = "Pos" [1] 7 Joining, by = "Pos" [1] 8 Joining, by = "Pos" [1] 9 Joining, by = "Pos" [1] 10 Joining, by = "Pos" [1] 11 Joining, by = "Pos" [1] 12 Joining, by = "Pos" [1] 13 Joining, by = "Pos" [1] 14 Joining, by = "Pos" [1] 15 Joining, by = "Pos" [1] 16 Joining, by = "Pos" [1] 17 Joining, by = "Pos" [1] 18 Joining, by = "Pos" [1] 19 Joining, by = "Pos" [1] 20 Joining, by = "Pos" [1] 21 Joining, by = "Pos" [1] 22 Joining, by = "Pos" [1] 23 Joining, by = "Pos" [1] 24 Joining, by = "Pos" [1] 25 Joining, by = "Pos" [1] 26 Joining, by = "Pos" [1] 27 Joining, by = "Pos" [1] 28 Joining, by = "Pos" [1] 29 Joining, by = "Pos" [1] 30 Joining, by = "Pos" [1] 31 Joining, by = "Pos" [1] 32 Joining, by = "Pos" [1] 33 Joining, by = "Pos" [1] 34 Joining, by = "Pos" [1] 35 Joining, by = "Pos" [1] 36 Joining, by = "Pos" [1] 37 Joining, by = "Pos" [1] 38 Joining, by = "Pos" [1] 39 Joining, by = "Pos" [1] 40 Joining, by = "Pos" [1] 41 Joining, by = "Pos" [1] 42 Joining, by = "Pos" [1] 43 Joining, by = "Pos" [1] 44 Joining, by = "Pos" [1] 45 Joining, by = "Pos" [1] 46 Joining, by = "Pos" [1] 47 Joining, by = "Pos" [1] 48 Joining, by = "Pos" [1] 49 Joining, by = "Pos" [1] 50 Joining, by = "Pos" [1] 51 Joining, by = "Pos" [1] 52 Joining, by = "Pos" [1] 53 Joining, by = "Pos" [1] 54 Joining, by = "Pos" [1] 55 Joining, by = "Pos" [1] 56 Joining, by = "Pos" [1] 57 Joining, by = "Pos" [1] 58 Joining, by = "Pos" [1] 59 Joining, by = "Pos" [1] 60 Joining, by = "Pos" [1] 61 Joining, by = "Pos" [1] 62 Joining, by = "Pos" [1] 63 Joining, by = "Pos" [1] 64 Joining, by = "Pos" [1] 65 Joining, by = "Pos" [1] 66 Joining, by = "Pos" [1] 67 Joining, by = "Pos" [1] 68 Joining, by = "Pos" [1] 69 Joining, by = "Pos" [1] 70 Joining, by = "Pos" [1] 71 Joining, by = "Pos" [1] 72 Joining, by = "Pos" [1] 73 Joining, by = "Pos" [1] 74 Joining, by = "Pos" [1] 75 Joining, by = "Pos" [1] 76 Joining, by = "Pos" [1] 77 Joining, by = "Pos" [1] 78 Joining, by = "Pos" [1] 79 Joining, by = "Pos" [1] 80 Joining, by = "Pos" [1] 81 Joining, by = "Pos" [1] 82 Joining, by = "Pos" [1] 83 Joining, by = "Pos" [1] 84 Joining, by = "Pos" [1] 85 Joining, by = "Pos" [1] 86 Joining, by = "Pos" [1] 87 Joining, by = "Pos" [1] 88 Joining, by = "Pos" [1] 89 Joining, by = "Pos" [1] 90 Joining, by = "Pos" [1] 91 Joining, by = "Pos" [1] 92 Joining, by = "Pos" [1] 93 Joining, by = "Pos" [1] 94 Joining, by = "Pos" [1] 95 Joining, by = "Pos" [1] 96 Joining, by = "Pos" [1] 97 Joining, by = "Pos" [1] 98 Joining, by = "Pos" [1] 99 Joining, by = "Pos" [1] 100 Joining, by = "Pos" [1] "Binning read counts by gene boundaries" converting counts to integer mode Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 3 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing log2 fold change (MLE): condition ATCC vs Expected Wald test p-value: condition ATCC vs Expected DataFrame with 6 rows and 6 columns baseMean log2FoldChange lfcSE stat pvalue padj 2 1164.44 -10.313625 0.855152 -12.060573 1.70591e-33 1.14354e-32 3 1203.22 -7.633786 0.424323 -17.990525 2.31157e-72 5.88133e-71 4 1064.41 0.312466 0.275188 1.135462 2.56182e-01 3.14939e-01 5 1119.23 -1.403466 0.246877 -5.684874 1.30909e-08 3.88666e-08 6 1083.34 0.165843 0.245310 0.676056 4.99005e-01 5.66347e-01 7 1020.78 0.792066 0.242236 3.269806 1.07621e-03 2.09206e-03 Package 'mclust' version 5.4.7 Type 'citation("mclust")' for citing this R package in publications. Attaching package: ‘mclust’ The following object is masked from ‘package:purrr’: map ---------------------------------------------------- Gaussian finite mixture model fitted by EM algorithm ---------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4290.477 2010 5 -8618.983 -8737.891 Clustering table: 1 2 580 1430 Mixing probabilities: 1 2 0.2987857 0.7012143 Means: 1 2 -6.647645 0.340288 Variances: 1 2 8.2414153 0.6848166 ------------------------------------------------------- Density estimation via Gaussian finite mixture modeling ------------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4290.476 2010 5 -8618.982 -8737.875 null device 1 [1] "Reduced" "Reduced" "Unchanged" "Unchanged" "Unchanged" "Unchanged" [7] "Unchanged" "Unchanged" "Unchanged" "Unchanged" converting counts to integer mode Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 3 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895 log2 fold change (MAP): condition Expected vs ATCC Wald test p-value: condition Expected vs ATCC DataFrame with 6 rows and 5 columns baseMean log2FoldChange lfcSE pvalue padj 2 1164.44 10.175449 0.835187 1.70591e-33 1.14354e-32 3 1203.22 7.590561 0.424654 2.31157e-72 5.88133e-71 4 1064.41 -0.290138 0.264867 2.56182e-01 3.14939e-01 5 1119.23 1.363215 0.249898 1.30909e-08 3.88666e-08 6 1083.34 -0.155698 0.238015 4.99005e-01 5.66347e-01 7 1020.78 -0.756215 0.236528 1.07621e-03 2.09206e-03 ---------------------------------------------------- Gaussian finite mixture model fitted by EM algorithm ---------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4191.933 2010 5 -8421.894 -8527.016 Clustering table: 1 2 1434 576 Mixing probabilities: 1 2 0.7054493 0.2945507 Means: 1 2 -0.3129835 6.6218511 Variances: 1 2 0.611051 7.833559 ------------------------------------------------------- Density estimation via Gaussian finite mixture modeling ------------------------------------------------------- Mclust V (univariate, unequal variance) model with 2 components: log-likelihood n df BIC ICL -4191.933 2010 5 -8421.895 -8527.026 null device 1 [1] "Reduced" "Reduced" "Unchanged" "Unchanged" "Unchanged" "Unchanged" [7] "Unchanged" "Unchanged" "Unchanged" "Unchanged"