基因数据处理20之BWASW算法ref分块建立索引然后比对

来源：互联网发布：苹果6激活应用与数据编辑：程序博客网时间：2024/05/17 15:39

SRR003161h20.fastq <span style="font-family: Arial, Helvetica, sans-serif; font-size: 12px; background-color: rgb(255, 255, 255);">三次测试：</span>

hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq >SRR003161h20BWASWchr1.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq[main] Real time: 0.315 sec; CPU: 0.257 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq >SRR003161h20BWASWchr1.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq[main] Real time: 0.306 sec; CPU: 0.251 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq >SRR003161h20BWASWchr1.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h20.fastq[main] Real time: 0.312 sec; CPU: 0.253 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq >SRR003161h20BWASWchr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq[main] Real time: 0.293 sec; CPU: 0.239 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq >SRR003161h20BWASWchr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq[main] Real time: 0.287 sec; CPU: 0.238 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq >SRR003161h20BWASWchr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h20.fastq[main] Real time: 0.293 sec; CPU: 0.240 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq >SRR003161h20BWASWchr1chr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq[main] Real time: 0.693 sec; CPU: 0.598 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq >SRR003161h20BWASWchr1chr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq[main] Real time: 0.646 sec; CPU: 0.588 sechadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq >SRR003161h20BWASWchr1chr2.sam[M::bwa_idx_load_from_disk] read 0 ALT contigs[bsw2_aln] read 5 sequences/pairs (2691 bp) ...[main] Version: 0.7.13-r1126[main] CMD: bwa bwasw GRCH38chr1chr2L7016431.fna SRR003161h20.fastq[main] Real time: 0.639 sec; CPU: 0.582 sec

只对两个串比较，时间较短，差不多查找比对时间可以减半

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