Loading required package: ggplot2 Loading required package: gridExtra Loading required package: dada2 Loading required package: Rcpp Loading required package: phyloseq Loading required package: DECIPHER Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:gridExtra’: combine 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, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:phyloseq’: distance Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: RSQLite Loading required package: phangorn Loading required package: ape Attaching package: ‘ape’ The following object is masked from ‘package:Biostrings’: complement ggplot2 gridExtra dada2 phyloseq DECIPHER phangorn TRUE TRUE TRUE TRUE TRUE TRUE R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] phangorn_2.5.5 ape_5.3 DECIPHER_2.12.0 [4] RSQLite_2.1.5 Biostrings_2.52.0 XVector_0.24.0 [7] IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0 [10] phyloseq_1.28.0 dada2_1.12.1 Rcpp_1.0.2 [13] gridExtra_2.3 ggplot2_3.2.1 BiocStyle_2.12.0 [16] knitr_1.24 loaded via a namespace (and not attached): [1] nlme_3.1-142 bitops_1.0-6 [3] matrixStats_0.55.0 bit64_0.9-7 [5] RColorBrewer_1.1-2 GenomeInfoDb_1.20.0 [7] tools_3.6.2 backports_1.1.4 [9] R6_2.4.0 vegan_2.5-6 [11] DBI_1.1.0 lazyeval_0.2.2 [13] mgcv_1.8-31 colorspace_1.4-1 [15] permute_0.9-5 ade4_1.7-13 [17] withr_2.1.2 tidyselect_0.2.5 [19] bit_1.1-14 compiler_3.6.2 [21] Biobase_2.44.0 DelayedArray_0.10.0 [23] scales_1.0.0 quadprog_1.5-7 [25] stringr_1.4.0 digest_0.6.20 [27] Rsamtools_2.0.3 rmarkdown_1.14 [29] pkgconfig_2.0.2 htmltools_0.3.6 [31] rlang_0.4.2 hwriter_1.3.2 [33] jsonlite_1.6 BiocParallel_1.18.1 [35] dplyr_0.8.3 RCurl_1.95-4.12 [37] magrittr_1.5 GenomeInfoDbData_1.2.1 [39] biomformat_1.12.0 Matrix_1.2-18 [41] munsell_0.5.0 Rhdf5lib_1.6.2 [43] stringi_1.4.3 yaml_2.2.0 [45] MASS_7.3-51.4 SummarizedExperiment_1.14.1 [47] zlibbioc_1.30.0 rhdf5_2.28.1 [49] plyr_1.8.4 grid_3.6.2 [51] blob_1.2.0 crayon_1.3.4 [53] lattice_0.20-38 splines_3.6.2 [55] multtest_2.40.0 zeallot_0.1.0 [57] pillar_1.4.2 igraph_1.2.4.1 [59] GenomicRanges_1.36.1 reshape2_1.4.3 [61] codetools_0.2-16 fastmatch_1.1-0 [63] glue_1.3.1 evaluate_0.14 [65] ShortRead_1.42.0 latticeExtra_0.6-28 [67] data.table_1.12.2 BiocManager_1.30.4 [69] RcppParallel_4.4.4 vctrs_0.2.0 [71] foreach_1.4.7 gtable_0.3.0 [73] purrr_0.3.3 assertthat_0.2.1 [75] xfun_0.8 survival_3.1-8 [77] tibble_2.1.3 iterators_1.0.12 [79] GenomicAlignments_1.20.1 memoise_1.1.0 [81] cluster_2.1.0 trying URL 'http://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip' Content type 'application/zip' length 36910055 bytes (35.2 MB) ================================================== downloaded 35.2 MB Archive: data/MiSeqSOPData.zip inflating: data/MiSeq_SOP/F3D0_S188_L001_R1_001.fastq creating: data/__MACOSX/ creating: data/__MACOSX/MiSeq_SOP/ inflating: data/__MACOSX/MiSeq_SOP/._F3D0_S188_L001_R1_001.fastq inflating: data/MiSeq_SOP/F3D0_S188_L001_R2_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._F3D0_S188_L001_R2_001.fastq inflating: data/MiSeq_SOP/F3D141_S207_L001_R1_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._F3D141_S207_L001_R1_001.fastq inflating: data/MiSeq_SOP/F3D141_S207_L001_R2_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._F3D141_S207_L001_R2_001.fastq inflating: data/MiSeq_SOP/F3D142_S208_L001_R1_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._F3D142_S208_L001_R1_001.fastq inflating: 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data/__MACOSX/MiSeq_SOP/._F3D9_S197_L001_R2_001.fastq inflating: data/MiSeq_SOP/HMP_MOCK.v35.fasta inflating: data/__MACOSX/MiSeq_SOP/._HMP_MOCK.v35.fasta inflating: data/MiSeq_SOP/Mock_S280_L001_R1_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._Mock_S280_L001_R1_001.fastq inflating: data/MiSeq_SOP/Mock_S280_L001_R2_001.fastq inflating: data/__MACOSX/MiSeq_SOP/._Mock_S280_L001_R2_001.fastq inflating: data/MiSeq_SOP/mouse.dpw.metadata inflating: data/__MACOSX/MiSeq_SOP/._mouse.dpw.metadata inflating: data/MiSeq_SOP/mouse.time.design inflating: data/__MACOSX/MiSeq_SOP/._mouse.time.design inflating: data/MiSeq_SOP/stability.batch inflating: data/__MACOSX/MiSeq_SOP/._stability.batch inflating: data/MiSeq_SOP/stability.files inflating: data/__MACOSX/MiSeq_SOP/._stability.files Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. Error in dada(derepFs[1:40], err = NULL, selfConsist = TRUE) : The derep argument must be a derep-class object, list of derep-class objects, or a character vector of fastq filenames. Execution halted