[build] loading fasta file refs/ERCC92.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 91 target sequences
[build] warning: replaced 1 non-ACGUT characters in the input sequence
        with pseudorandom nucleotides
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 92 contigs and contains 77828 k-mers 


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/HBR_3_R1.fq
                             reads/HBR_3_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 129,786 reads, 61,351 reads pseudoaligned
[quant] estimated average fragment length: 169.04
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/HBR_1_R1.fq
                             reads/HBR_1_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 118,571 reads, 55,972 reads pseudoaligned
[quant] estimated average fragment length: 170.53
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/HBR_2_R1.fq
                             reads/HBR_2_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 144,826 reads, 68,717 reads pseudoaligned
[quant] estimated average fragment length: 164.791
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/UHR_2_R1.fq
                             reads/UHR_2_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 162,373 reads, 79,050 reads pseudoaligned
[quant] estimated average fragment length: 169.332
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/UHR_1_R1.fq
                             reads/UHR_1_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 227,392 reads, 118,328 reads pseudoaligned
[quant] estimated average fragment length: 180.392
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 92
[index] number of k-mers: 77,828
[index] number of equivalence classes: 92
[quant] running in paired-end mode
[quant] will process pair 1: reads/UHR_3_R1.fq
                             reads/UHR_3_R2.fq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 185,442 reads, 98,297 reads pseudoaligned
[quant] estimated average fragment length: 167.16
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 52 rounds

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

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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’

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