Using tophat2 installation at
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/tophat2
TopHat v2.0.10
Using bowtie installation at
/data/results/tools/align/bowtie2-2.1.0/bowtie2
/data/results/tools/align/bowtie2-2.1.0/bowtie2-align version 2.1.0
64-bit
Built on do-dmxp-mac.win.ad.jhu.edu
Tue Feb 26 13:34:02 EST 2013
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
Options: -O3 -m64 -msse2 -funroll-loops -g3 
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
22471256 reads; of these:
  22471256 (100.00%) were unpaired; of these:
    3875911 (17.25%) aligned 0 times
    10025960 (44.62%) aligned exactly 1 time
    8569385 (38.13%) aligned >1 times
82.75% overall alignment rate
[bam_sort_core] merging from 14 files...
[bam_sort_core] merging from 16 files...
[sam_header_read2] 22 sequences loaded.
18499841 uniq. mapped reads
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
21097935 reads; of these:
  21097935 (100.00%) were unpaired; of these:
    1226727 (5.81%) aligned 0 times
    11988109 (56.82%) aligned exactly 1 time
    7883099 (37.36%) aligned >1 times
94.19% overall alignment rate
[bam_sort_core] merging from 14 files...
[bam_sort_core] merging from 16 files...
[sam_header_read2] 22 sequences loaded.
19739614 uniq. mapped reads
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
16956026 reads; of these:
  16956026 (100.00%) were unpaired; of these:
    1112853 (6.56%) aligned 0 times
    8547535 (50.41%) aligned exactly 1 time
    7295638 (43.03%) aligned >1 times
93.44% overall alignment rate
[bam_sort_core] merging from 12 files...
[bam_sort_core] merging from 16 files...
[sam_header_read2] 22 sequences loaded.
15750260 uniq. mapped reads
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
15020967 reads; of these:
  15020967 (100.00%) were unpaired; of these:
    888841 (5.92%) aligned 0 times
    8884199 (59.15%) aligned exactly 1 time
    5247927 (34.94%) aligned >1 times
94.08% overall alignment rate
[bam_sort_core] merging from 11 files...
[bam_sort_core] merging from 16 files...
[sam_header_read2] 22 sequences loaded.
14060711 uniq. mapped reads