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.
12389975 reads; of these:
  12389975 (100.00%) were unpaired; of these:
    874113 (7.06%) aligned 0 times
    3675543 (29.67%) aligned exactly 1 time
    7840319 (63.28%) aligned >1 times
92.94% overall alignment rate
[bam_sort_core] merging from 9 files...
[bam_sort_core] merging from 24 files...
[sam_header_read2] 22 sequences loaded.
26087787 uniq. mapped reads
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
14843900 reads; of these:
  14843900 (100.00%) were unpaired; of these:
    967000 (6.51%) aligned 0 times
    3253641 (21.92%) aligned exactly 1 time
    10623259 (71.57%) aligned >1 times
93.49% overall alignment rate
[bam_sort_core] merging from 10 files...
[bam_sort_core] merging from 24 files...
[sam_header_read2] 22 sequences loaded.
24573182 uniq. mapped reads