******************************************************* Rscript /opt/trax/checkRmodules.R DESeq2 Loading required package: S4Vectors Loading required package: stats4 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 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 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: ‘matrixStats’ The following objects are masked from ‘package:Biobase’: anyMissing, rowMedians Loading required package: BiocParallel Attaching package: ‘DelayedArray’ The following objects are masked from ‘package:matrixStats’: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from ‘package:base’: aperm, apply, rowsum Attaching package: ‘plyr’ The following object is masked from ‘package:matrixStats’: count The following object is masked from ‘package:IRanges’: desc The following object is masked from ‘package:S4Vectors’: rename Attaching package: ‘gridExtra’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:BiocGenerics’: combine ******************************************************* Rscript /opt/trax//featuretypes.R phloemleaf4/phloemleaf4-mapinfo.txt phloemleaf4/phloemleaf4-mapinfo.pdf Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'phloemleaf4/phloemleaf4-mapinfo.txt': No such file or directory Execution halted /opt/trax//featuretypes.R failed ******************************************************* Rscript /opt/trax//pcareadcounts.R phloemleaf4/phloemleaf4-readcounts.txt samplefile.txt phloemleaf4/phloemleaf4-pca.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//pcareadcounts.R phloemleaf4/phloemleaf4-trnacounts.txt samplefile.txt phloemleaf4/phloemleaf4-pcatrna.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//analyzecounts.R phloemleaf4 phloemleaf4/phloemleaf4-readcounts.txt samplefile.txt samplepairs.txt Loading required package: S4Vectors Loading required package: stats4 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 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 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: ‘matrixStats’ The following objects are masked from ‘package:Biobase’: anyMissing, rowMedians Loading required package: BiocParallel Attaching package: ‘DelayedArray’ The following objects are masked from ‘package:matrixStats’: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from ‘package:base’: aperm, apply, rowsum Attaching package: ‘gridExtra’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:BiocGenerics’: combine Attaching package: ‘plyr’ The following object is masked from ‘package:matrixStats’: count The following object is masked from ‘package:IRanges’: desc The following object is masked from ‘package:S4Vectors’: rename Warning message: In read.table(args[4], stringsAsFactors = FALSE) : incomplete final line found by readTableHeader on 'samplepairs.txt' using pre-existing size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Saving 7 x 7 in image Warning messages: 1: Removed 501 rows containing missing values (geom_point). 2: Removed 501 rows containing missing values (geom_text_repel). ******************************************************* Rscript /opt/trax//makescatter.R phloemleaf4 phloemleaf4/phloemleaf4-normalizedreadcounts.txt ath-trnatable.txt phloemleaf4/phloemleaf4-genetypes.txt samplefile.txt samplepairs.txt Warning message: In read.table(args[6], stringsAsFactors = FALSE) : incomplete final line found by readTableHeader on 'samplepairs.txt' [1] "trna_fiveprime" "trna_threeprime" "trna_other" "trna_wholecounts" [5] "tRNA" "snoRNA" "miRNA" "Mt_tRNA" [9] "rRNA" "Mt_rRNA" "snRNA" Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//endplot.R --ends=phloemleaf4/phloemleaf4-trnaendcounts.txt --trna=ath-trnatable.txt --samples=samplefile.txt --directory=phloemleaf4/mismatch/ Fatal error: cannot open file '/opt/trax//endplot.R': No such file or directory /opt/trax//endplot.R failed ******************************************************* Rscript /opt/trax//featuretypes.R phloemleaf4/phloemleaf4-typecounts.txt phloemleaf4/phloemleaf4-typecounts.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//featuretypes.R phloemleaf4/phloemleaf4-aminocounts.txt phloemleaf4/phloemleaf4-aminocounts.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//featuretypesreal.R phloemleaf4/phloemleaf4-aminocounts.txt phloemleaf4/phloemleaf4-aminocounts.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//featuretypesreal.R phloemleaf4/phloemleaf4-typerealcounts.txt phloemleaf4/phloemleaf4-typerealcounts.pdf Saving 7 x 7 in image ******************************************************* Rscript /opt/trax//readlengthhistogram.R phloemleaf4/phloemleaf4-readlengths.txt phloemleaf4/phloemleaf4-readlengths.pdf Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. Warning messages: 1: Use of `binnedlengths$bin` is discouraged. Use `bin` instead. 2: Use of `binnedlengths$value` is discouraged. Use `value` instead. 3: Use of `binnedlengths$variable` is discouraged. Use `variable` instead. Warning messages: 1: Use of `binnedlengths$bin` is discouraged. Use `bin` instead. 2: Use of `binnedlengths$value` is discouraged. Use `value` instead. 3: Use of `binnedlengths$variable` is discouraged. Use `variable` instead. ******************************************************* Rscript /opt/trax//newcoverageplots.R --cov=phloemleaf4/phloemleaf4-coverage.txt --locicov=phloemleaf4/pretRNAs/phloemleaf4-pretRNAcoverage.txt --trna=ath-trnatable.txt --samples=samplefile.txt --allcov=phloemleaf4/phloemleaf4-coverage.pdf --runname=phloemleaf4 --modomics=ath-modomics.txt --combinecov=phloemleaf4/phloemleaf4-combinecoverage.pdf --directory=phloemleaf4 Saving 7 x 7 in image Warning message: Removed 44240 rows containing missing values (position_stack). ******************************************************* Rscript /opt/trax//boxplotmismatches.R --runname=phloemleaf4 --mismatch=phloemleaf4/phloemleaf4-coverage.txt --trna=ath-trnatable.txt --samples=samplefile.txt --directory=phloemleaf4/mismatch/ Warning message: Removed 1152 rows containing missing values (geom_point). Warning message: Removed 1152 rows containing missing values (geom_point). Warning message: Removed 54 rows containing missing values (geom_point). Warning message: Removed 54 rows containing missing values (geom_point). Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image There were 21 warnings (use warnings() to see them) There were 50 or more warnings (use warnings() to see the first 50)