Using tophat2 installation at
/data/results/tools/align/tophat-2.0.12.Linux_x86_64/tophat2
TopHat v2.0.12
Using bowtie installation at
/data/results/tools/align/bowtie2-2.2.3/bowtie2
/data/results/tools/align/bowtie2-2.2.3/bowtie2-align-s version 2.2.3
64-bit
Built on do-dmxp-mac.win.ad.jhu.edu
Thu May 29 17:14:09 EDT 2014
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
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.
18539178 reads; of these:
  18539178 (100.00%) were unpaired; of these:
    1715855 (9.26%) aligned 0 times
    5914149 (31.90%) aligned exactly 1 time
    10909174 (58.84%) aligned >1 times
90.74% overall alignment rate
[bam_sort_core] merging from 12 files...
[bam_sort_core] merging from 32 files...
[sam_header_read2] 22 sequences loaded.
40965050 uniq. mapped reads
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
20570121 reads; of these:
  20570121 (100.00%) were unpaired; of these:
    1665602 (8.10%) aligned 0 times
    5931301 (28.83%) aligned exactly 1 time
    12973218 (63.07%) aligned >1 times
91.90% overall alignment rate
[bam_sort_core] merging from 14 files...
[bam_sort_core] merging from 32 files...
[sam_header_read2] 22 sequences loaded.
42063858 uniq. mapped reads