Warning: Output file 'chip,low' was specified without -S.  This will not work in future HISAT 2 versions.  Please use -S instead.
17844468 reads; of these:
  17844468 (100.00%) were paired; of these:
    8631681 (48.37%) aligned concordantly 0 times
    7635442 (42.79%) aligned concordantly exactly 1 time
    1577345 (8.84%) aligned concordantly >1 times
    ----
    8631681 pairs aligned concordantly 0 times; of these:
      29858 (0.35%) aligned discordantly 1 time
    ----
    8601823 pairs aligned 0 times concordantly or discordantly; of these:
      17203646 mates make up the pairs; of these:
        16447032 (95.60%) aligned 0 times
        680389 (3.95%) aligned exactly 1 time
        76225 (0.44%) aligned >1 times
53.92% overall alignment rate