bwa 建立索引

作者: dming1024 | 来源:发表于2019-06-08 21:42 被阅读0次

WES2Neoantigen Pipeline
bwa 建立索引
FASTQ格式-摘录
bwa比对
使用bwa 批量比对整个文件夹的fasta文件
BWA： Parse error reading genome.
线粒体组装
搜索引擎Lucene（4）：索引的创建过程
联合索引-以及如何使用索引
bwa bowtie2 salmon subread hisat

bowtie2和hisat2的索引在网上都可以下载得到，但是bwa的索引我怎么都没找到，没办法只能自己搞起来。之前用个2核4G的服务器，怎么都建立不起来这个索引，总是溢出内存，最后还是选了个4核8G的服务器，时间还是要了60多分钟，跑的很勉强。

time bwa index hg19.fa
[bwa_index] Pack FASTA... 30.89 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6191387966, availableWord=447648912
[BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999998 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999998 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999998 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999998 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999998 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999998 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999998 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999998 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999998 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999998 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999998 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999998 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999998 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999998 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999998 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999998 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999998 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999998 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999998 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999998 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999998 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999998 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999998 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999998 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999998 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999998 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999998 characters processed.
[BWTIncConstructFromPacked] 310 iterations done. 3099999998 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3199999998 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999998 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999998 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3499999998 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3599999998 characters processed.
[BWTIncConstructFromPacked] 370 iterations done. 3699999998 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3799999998 characters processed.
[BWTIncConstructFromPacked] 390 iterations done. 3899999998 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 3999999998 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4099999998 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999998 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999998 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999998 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999998 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999998 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999998 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999998 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999998 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999998 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999998 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5199999998 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5299999998 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5399999998 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5499999998 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5596003406 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5681458862 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5757407918 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5824907614 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5884897502 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5938212670 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5985595326 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6027705102 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6065128334 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6098386190 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6127941854 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6154206942 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
[bwt_gen] Finished constructing BWT in 687 iterations.
[bwa_index] 2552.60 seconds elapse.
[bwa_index] Update BWT... 16.77 sec
[bwa_index] Pack forward-only FASTA... 24.22 sec
[bwa_index] Construct SA from BWT and Occ... 1277.84 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index hg19.fa
[main] Real time: 4048.577 sec; CPU: 3902.327 sec

real    67m28.580s
user    64m43.695s
sys 0m18.633s