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：
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr1.sam 264 + 0 in total (QC-passed reads + QC-Failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 105 + 0 mapped (39.77% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr2.sam 260 + 0 in total (QC-passed reads + QC-Failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 83 + 0 mapped (31.92% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr3.sam 256 + 0 in total (QC-passed reads + QC-Failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 80 + 0 mapped (31.25% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr4.sam 254 + 0 in total (QC-passed reads + QC-Failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 58 + 0 mapped (22.83% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub$ samtools flagstat SRR003161h1000chr1-4.sam 264 + 0 in total (QC-passed reads + QC-Failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 146 + 0 mapped (55.30% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)3.比对结果文件，太长，就不粘了
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