bowtie2软件构建基因组索引准备好基因组的⽂件及hg19.fa，然后调⽤bowtie2。
#hg19.fa 基因组fa⽂件
#hg19 索引前缀
#bowtie2-build 构建参考基因组索引⽂件
$bowtie2-build hg19/hg19.fa hg19/hg19
Settings:
Output files: 'hg19/hg19.*.bt2'
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offt rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Asrtions: disabled
Random ed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
hg19/hg19.fa
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:17
Calculating joined length
Writing header
Rerving space for joined string
Joining reference quences
Time to join reference quences: 00:00:12
超星学习通登录入口
bmax according to bmaxDivN tting: 715331782
Using parameters --bmax 536498837 --dcv 1024
Doing ahead-of-time memory usage test
Pasd! Constructing with the parameters: --bmax 536498837 --dcv 1024 Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:01:22
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:24
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:43
Sanity-checking and returning
Building samples
Rerving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offts, eliminating duplicates
QSorting sample offts, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.86133e+09 (target: 536498836)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
No samples; asmbling all-inclusive block
Sorting block of length 2861327131 for bucket 1
(Using difference cover)
Sorting block time: 00:44:25
Returning block of 2861327132 for bucket 1
什么的空气填词语
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 844862932
fchr[G]: 1429875684
fchr[T]: 2015233940
fchr[$]: 2861327131
Exiting Ebwt::buildToDisk()
pursueReturning from initFromVector
Wrote 957974502 bytes to primary EBWT file: hg19/hg19.1.bt2 Wrote 715331788 bytes to condary EBWT file: hg19/hg19.2.bt2 Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2861327131
bwtLen: 2861327132
叶静怡
sz: 715331783
bwtSz: 715331783
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 178832946
offsSz: 715331784
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 14902746
numLines: 14902746
ebwtTotLen: 953775744
ebwtTotSz: 953775744
color: 0
痕迹读音rever: 0
Total time for call to driver() for forward index: 00:56:27
Reading reference sizes
Time reading reference sizes: 00:00:13
Calculating joined length
Writing header
Rerving space for joined string
Joining reference quences
Time to join reference quences: 00:00:11
Time to rever reference quence: 00:00:02
bmax according to bmaxDivN tting: 715331782
Using parameters --bmax 536498837 --dcv 1024
Doing ahead-of-time memory usage test
Pasd! Constructing with the parameters: --bmax 536498837 --dcv 1024 Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:01:29
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:28
七拼八凑
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:42
Sanity-checking and returning
Building samples
Rerving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offts, eliminating duplicates
QSorting sample offts, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.86133e+09 (target: 536498836)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
百发百中的反义词
No samples; asmbling all-inclusive block
Sorting block of length 2861327131 for bucket 1
(Using difference cover)
Sorting block time: 00:44:02
Returning block of 2861327132 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 844862932
fchr[G]: 1429875684
fchr[T]: 2015233940
fchr[$]: 2861327131
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 957974502 bytes to primary EBWT file: v.1.bt2 Wrote 715331788 bytes to condary EBWT file: v.2.bt2 Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:开广
len: 2861327131
bwtLen: 2861327132
sz: 715331783
bwtSz: 715331783
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
