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)
Offset 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
Assertions: disabled
Random seed: 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
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:12
bmax according to bmaxDivN setting: 715331782
Using parameters --bmax 536498837 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these 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
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, 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; assembling 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
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: hg19/hg19.1.bt2
Wrote 715331788 bytes to secondary EBWT file: hg19/hg19.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2861327131
bwtLen: 2861327132
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
reverse: 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
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:11
Time to reverse reference sequence: 00:00:02
bmax according to bmaxDivN setting: 715331782
Using parameters --bmax 536498837 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these 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
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:42
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, 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; assembling 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: hg19/hg19.rev.1.bt2
Wrote 715331788 bytes to secondary EBWT file: hg19/hg19.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2861327131
bwtLen: 2861327132
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
reverse: 1
Total time for backward call to driver() for mirror index: 00:56:19
花费一个小时左右。
结果：
跑完之后可以保存，直接调用就可以了。pwd确定文件目录的路径
#直接拷贝构建好的bowtie2索引
cp /home/training58/hicpro/hg19.*bt2 ./hg19