bowtie2 paired-end alignment

Bowtie 2 version 2.2.6 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x  {-1  -2  | -U } [-S ]
time bowtie2 -p 8 -x reference/human/hg19 -1 input_1.fastq -2 input_2.fastq > output.sam
48755614 reads; of these:
  48755614 (100.00%) were paired; of these:
    24164921 (49.56%) aligned concordantly 0 times
    14767863 (30.29%) aligned concordantly exactly 1 time
    9822830 (20.15%) aligned concordantly >1 times
    ----
    24164921 pairs aligned concordantly 0 times; of these:
      4355288 (18.02%) aligned discordantly 1 time
    ----
    19809633 pairs aligned 0 times concordantly or discordantly; of these:
      39619266 mates make up the pairs; of these:
        27256949 (68.80%) aligned 0 times
        8927823 (22.53%) aligned exactly 1 time
        3434494 (8.67%) aligned >1 times
72.05% overall alignment rate

real	44m49.082s
product: Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz
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