基因数据处理23之BWASW算法ref分块建立索引然后比对（ref切分为

结论：

read为25000条对单条染色体进行比对需要110秒左右，对chr1-4比对需要160秒左右

运行结果：

1
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 112.181 sec; CPU: 111.624 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 112.011 sec; CPU: 111.420 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 110.261 sec; CPU: 109.677 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 111.889 sec; CPU: 111.312 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 160.292 sec; CPU: 150.078 sec
26513 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10339 + 0 mapped (39.00% : 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)
26514 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10442 + 0 mapped (39.38% : 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)
26478 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9833 + 0 mapped (37.14% : 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)
26436 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9658 + 0 mapped (36.53% : 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)
26558 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14808 + 0 mapped (55.76% : 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)
2
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 114.615 sec; CPU: 111.628 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 113.653 sec; CPU: 113.072 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 112.748 sec; CPU: 110.745 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 111.248 sec; CPU: 110.677 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 159.363 sec; CPU: 149.086 sec
26513 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10339 + 0 mapped (39.00% : 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)
26514 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10442 + 0 mapped (39.38% : 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)
26478 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9833 + 0 mapped (37.14% : 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)
26436 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9658 + 0 mapped (36.53% : 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)
26558 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14808 + 0 mapped (55.76% : 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
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 115.228 sec; CPU: 112.824 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 112.081 sec; CPU: 111.251 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 112.233 sec; CPU: 110.827 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 111.987 sec; CPU: 111.213 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 159.284 sec; CPU: 148.896 sec
26513 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10339 + 0 mapped (39.00% : 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)
26514 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10442 + 0 mapped (39.38% : 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)
26478 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9833 + 0 mapped (37.14% : 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)
26436 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9658 + 0 mapped (36.53% : 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)
26558 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14808 + 0 mapped (55.76% : 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)

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