Read 1000000 spots for SRR3194430 Written 1000000 spots for SRR3194430 Read 1000000 spots for SRR3194428 Written 1000000 spots for SRR3194428 Read 1000000 spots for SRR3194431 Written 1000000 spots for SRR3194431 Read 1000000 spots for SRR3194429 Written 1000000 spots for SRR3194429 Read 1000000 spots for SRR3191543 Written 1000000 spots for SRR3191543 Read 1000000 spots for SRR3191544 Written 1000000 spots for SRR3191544 Read 1000000 spots for SRR3191545 Written 1000000 spots for SRR3191545 Read 1000000 spots for SRR3191542 Written 1000000 spots for SRR3191542 [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in single-end mode [quant] will process file 1: reads/SRR3194428.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 766,880 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 953 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in single-end mode [quant] will process file 1: reads/SRR3194430.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 746,893 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 941 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in single-end mode [quant] will process file 1: reads/SRR3194431.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 748,837 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,028 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in single-end mode [quant] will process file 1: reads/SRR3194429.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 775,929 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,079 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [~warn] you specified using a gaussian but have paired end data [~warn] we suggest omitting these parameters and let us estimate the distribution from data [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in paired-end mode [quant] will process pair 1: reads/SRR3191543_1.fastq reads/SRR3191543_2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 814,907 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 956 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [~warn] you specified using a gaussian but have paired end data [~warn] we suggest omitting these parameters and let us estimate the distribution from data [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in paired-end mode [quant] will process pair 1: reads/SRR3191544_1.fastq reads/SRR3191544_2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 793,510 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 913 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [~warn] you specified using a gaussian but have paired end data [~warn] we suggest omitting these parameters and let us estimate the distribution from data [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in paired-end mode [quant] will process pair 1: reads/SRR3191542_1.fastq reads/SRR3191542_2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 809,677 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,005 rounds [quant] fragment length distribution is truncated gaussian with mean = 187, sd = 70 [~warn] you specified using a gaussian but have paired end data [~warn] we suggest omitting these parameters and let us estimate the distribution from data [index] k-mer length: 31 [index] number of targets: 188,753 [index] number of k-mers: 109,544,288 [index] number of equivalence classes: 760,757 [quant] running in paired-end mode [quant] will process pair 1: reads/SRR3191545_1.fastq reads/SRR3191545_2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,000,000 reads, 794,223 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 975 rounds 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, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min 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: locfit locfit 1.5-9.1 2013-03-22 Loading required package: lattice Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess