基因数据处理21之BWASW算法ref分块建立索引然后比对（ref切分为
发布时间：2021-05-15 18:31:48 所属栏目：大数据 来源：网络整理
导读：1.时间分析 对ref为单条染色体进行比对，第一次比对在3-5s不等，对chr1-4比对，在20s左右 连续比对多次后，对单染色体比对降到1s左右，chr1-4降到2s左右 不懂为什么比一次比对时间比较长，后面几次比对时间变短 运行代码： hadoop@Master:~/cloud/adam/xubo/
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1.时间分析 对ref为单条染色体进行比对，第一次比对在3-5s不等，对chr1-4比对，在20s左右 连续比对多次后，对单染色体比对降到1s左右，chr1-4降到2s左右 不懂为什么比一次比对时间比较长，后面几次比对时间变短 运行代码： hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 2.885 sec; CPU: 1.118 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.068 sec; CPU: 1.022 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.068 sec; CPU: 1.017 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.068 sec; CPU: 1.019 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 2.511 sec; CPU: 1.056 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 0.999 sec; CPU: 0.950 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 1.017 sec; CPU: 0.964 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 1.009 sec; CPU: 0.965 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.071 sec; CPU: 1.019 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.072 sec; CPU: 1.015 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.068 sec; CPU: 1.018 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000chr1.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.065 sec; CPU: 1.017 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000chr1.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.070 sec; CPU: 1.017 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq >SRR003161h1000chr1.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h1000.fastq [main] Real time: 1.050 sec; CPU: 1.009 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000chr2.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 1.017 sec; CPU: 0.969 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000chr2.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 1.015 sec; CPU: 0.969 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq >SRR003161h1000chr2.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h1000.fastq [main] Real time: 1.023 sec; CPU: 0.966 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq >SRR003161h1000chr3.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq [main] Real time: 0.940 sec; CPU: 0.885 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq >SRR003161h1000chr3.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq [main] Real time: 0.933 sec; CPU: 0.888 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq >SRR003161h1000chr3.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h1000.fastq [main] Real time: 0.915 sec; CPU: 0.872 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq >SRR003161h1000chr4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq [main] Real time: 0.918 sec; CPU: 0.871 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq >SRR003161h1000chr4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq [main] Real time: 0.919 sec; CPU: 0.868 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq >SRR003161h1000chr4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h1000.fastq [main] Real time: 0.889 sec; CPU: 0.853 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 20.819 sec; CPU: 3.195 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 17.380 sec; CPU: 2.803 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 14.140 sec; CPU: 2.454 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 4.305 sec; CPU: 2.166 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 2.034 sec; CPU: 1.970 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 2.059 sec; CPU: 1.995 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 2.079 sec; CPU: 2.000 sec hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ rm SRR003161h1000chr1-4.sam hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq >SRR003161h1000chr1-4.sam [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 250 sequences/pairs (161179 bp) ... [main] Version: 0.7.13-r1126 [main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h1000.fastq [main] Real time: 2.046 sec; CPU: 1.997 sec 2.准确性分析： （编辑：厦门网） 【声明】本站内容均来自网络，其相关言论仅代表作者个人观点，不代表本站立场。若无意侵犯到您的权利，请及时与联系站长删除相关内容! |
