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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 #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 |
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来自： CharlesNice > 《bowtie2 微信文章》
