[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 345,691
[index] number of k-mers: 107,833,113
[index] number of equivalence classes: 613,105
[quant] running in paired-end mode
[quant] will process pair 1: /projects/btl/polya/encode/imr90/cytosol/rep1/reads/reads_1.fastq.gz
                             /projects/btl/polya/encode/imr90/cytosol/rep1/reads/reads_2.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] learning parameters for sequence specific bias
[quant] processed 114,006,059 reads, 34,422,354 reads pseudoaligned
[quant] estimated average fragment length: 380.857
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 2,496 rounds
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