基因数据处理24之BWASW算法ref分块建立索引然后比对（ref切分为

比默认的要块1倍左右

1
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 59.126 sec; CPU: 113.999 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 61.559 sec; CPU: 112.876 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 58.467 sec; CPU: 110.546 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 61.645 sec; CPU: 111.260 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 91.130 sec; CPU: 150.390 sec
26528 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10363 + 0 mapped (39.06% : 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)
26511 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10440 + 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)
26481 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9808 + 0 mapped (37.04% : 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)
26437 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9638 + 0 mapped (36.46% : 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)
26551 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14821 + 0 mapped (55.82% : 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 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 60.577 sec; CPU: 113.043 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 61.180 sec; CPU: 112.688 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 58.466 sec; CPU: 110.763 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 60.691 sec; CPU: 111.369 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 87.437 sec; CPU: 148.667 sec
26521 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10365 + 0 mapped (39.08% : 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)
26531 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10436 + 0 mapped (39.34% : 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)
26479 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9791 + 0 mapped (36.98% : 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)
26447 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9686 + 0 mapped (36.62% : 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)
26571 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14828 + 0 mapped (55.81% : 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 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr1L3556522.fna SRR003161h100000.fastq
[main] Real time: 62.541 sec; CPU: 112.986 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr2L3459909.fna SRR003161h100000.fastq
[main] Real time: 60.941 sec; CPU: 112.492 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr3L2832795.fna SRR003161h100000.fastq
[main] Real time: 58.108 sec; CPU: 110.632 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38chr4L2717352.fna SRR003161h100000.fastq
[main] Real time: 59.700 sec; CPU: 111.340 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 25000 sequences/pairs (14470082 bp) ...
[main] Version: 0.7.13-r1126
[main] CMD: bwa bwasw -t 4 GRCH38L12566578.fna SRR003161h100000.fastq
[main] Real time: 85.869 sec; CPU: 148.844 sec
26516 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10348 + 0 mapped (39.03% : 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)
26546 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
10474 + 0 mapped (39.46% : 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)
26479 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9803 + 0 mapped (37.02% : 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)
26459 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9690 + 0 mapped (36.62% : 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
14813 + 0 mapped (55.78% : 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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