基因数据处理15之scala对BWA运行结果进行时间提取

环境：

window?

eclpise 4.3.2

scala 2.10.4

正则表达式

提取代码：

package test
import scala.io.Source  
import java.io.File._
import java.io.PrintWriter
object logPatternBWA extends App {
val out=new PrintWriter("file/outDir.txt")
val source = Source.fromFile("file/bwaMcnode4T201603151254.txt").mkString  
println("*************")
val pattern = """(bwa aln|bwa samse)[^:]+:s*([0-9]*.[0-9]*)[^:]+:s*([0-9]*.[0-9]*)""".r 
val pattern2="""[bwa_aln_core]s*([0-9]+)s+sequences have been processed.n[main]""".r
// for(pattern(s1,num1,num2)<-pattern.findAllIn(source)) println("s1:"+s1+"  num1:"+num1+" num2:"+num2)
// for(pattern2(seq)<-pattern2.findAllIn(source)) println("seq:"+seq)
 val b1=for(pattern(s1,num2)<-pattern.findAllIn(source)) yield (s1,num2)
 val b2=for(pattern2(seq)<-pattern2.findAllIn(source)) yield (seq)
   
//  b2.foreach(println)
val b22=b2.toArray
val b11=b1.toArray
//while (b2.hasNext) println(b2.next)
 println("i: "+b11.length+" j:"+b22.length);
 for(k<-0 until b22.length) {
    println(b22(k)+","+b11(k)._1+","+b11(k)._2+","+b11(k)._3)
    out.println(b22(k)+","+b11(k)._3)
 }
 out.close()
// for(i<- 1 to 10;j<-1 to 4){
//   if (sum==10){
//    println("i: "+i+" j:"+j);
//    }else{
//      sum=sum+1
//    }
   
// }
//   val i = Array(1 to 10)
//   val j=Array(1 to 10)
//   val k1=for(k<-0 until i.length) yield (i(k),j(k))
//   k1.foreach(println)
//   for (k<-0 until i)

}

rm: cannot remove ‘SRR*’: No such file or directory
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 31.678 sec; CPU: 3.930 sec
[bwa_aln_core] convert to sequence coordinate... 6.08 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20t1.sai ../SRR003161h20.fastq
[main] Real time: 56.784 sec; CPU: 6.752 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.19 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 30.983 sec; CPU: 3.570 sec
[bwa_aln_core] convert to sequence coordinate... 5.56 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h1000t1.sai ../SRR003161h1000.fastq
[main] Real time: 49.933 sec; CPU: 6.212 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 6.07 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 67.352 sec; CPU: 9.489 sec
[bwa_aln_core] convert to sequence coordinate... 5.88 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.01 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h10000t1.sai ../SRR003161h10000.fastq
[main] Real time: 52.633 sec; CPU: 6.576 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 62.17 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 96.701 sec; CPU: 65.804 sec
[bwa_aln_core] convert to sequence coordinate... 5.73 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.08 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h100000t1.sai ../SRR003161h100000.fastq
[main] Real time: 56.368 sec; CPU: 6.749 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 31.007 sec; CPU: 3.347 sec
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20t2.sai ../SRR003161h20.fastq
[main] Real time: 50.984 sec; CPU: 6.232 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.19 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 34.497 sec; CPU: 3.582 sec
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h1000t2.sai ../SRR003161h1000.fastq
[main] Real time: 52.522 sec; CPU: 6.290 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 6.08 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 39.877 sec; CPU: 9.395 sec
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.01 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h10000t2.sai ../SRR003161h10000.fastq
[main] Real time: 54.645 sec; CPU: 6.288 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 62.09 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 95.003 sec; CPU: 65.583 sec
[bwa_aln_core] convert to sequence coordinate... 5.75 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.07 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h100000t2.sai ../SRR003161h100000.fastq
[main] Real time: 87.403 sec; CPU: 6.752 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 32.171 sec; CPU: 3.414 sec
[bwa_aln_core] convert to sequence coordinate... 5.67 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 5 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20t3.sai ../SRR003161h20.fastq
[main] Real time: 57.861 sec; CPU: 6.322 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.19 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 32.511 sec; CPU: 3.496 sec
[bwa_aln_core] convert to sequence coordinate... 5.55 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h1000t3.sai ../SRR003161h1000.fastq
[main] Real time: 55.078 sec; CPU: 6.212 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 6.09 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 42.617 sec; CPU: 9.430 sec
[bwa_aln_core] convert to sequence coordinate... 5.74 sec
[bwa_aln_core] refine gapped alignments... 0.67 sec
[bwa_aln_core] print alignments... 0.01 sec
[bwa_aln_core] 2500 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h10000t3.sai ../SRR003161h10000.fastq
[main] Real time: 112.531 sec; CPU: 6.439 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 62.33 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 104.038 sec; CPU: 65.953 sec
[bwa_aln_core] convert to sequence coordinate... 5.80 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.08 sec
[bwa_aln_core] 25000 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h100000t3.sai ../SRR003161h100000.fastq
[main] Real time: 64.331 sec; CPU: 6.806 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 692.43 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 697.70 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 581.75 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 595.36 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 601.15 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 137.42 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 3361.868 sec; CPU: 3316.962 sec
[bwa_aln_core] convert to sequence coordinate... 6.19 sec
[bwa_aln_core] refine gapped alignments... 2.57 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.90 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.62 sec
[bwa_aln_core] refine gapped alignments... 2.34 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.49 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.41 sec
[bwa_aln_core] refine gapped alignments... 2.27 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.44 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161t1.sai ../SRR003161.fastq
[main] Real time: 877.768 sec; CPU: 63.236 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 685.58 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 691.62 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 577.08 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 589.36 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 594.45 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 135.71 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 3402.127 sec; CPU: 3285.255 sec
[bwa_aln_core] convert to sequence coordinate... 6.10 sec
[bwa_aln_core] refine gapped alignments... 2.68 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.60 sec
[bwa_aln_core] refine gapped alignments... 2.61 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.52 sec
[bwa_aln_core] refine gapped alignments... 2.30 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.43 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.32 sec
[bwa_aln_core] refine gapped alignments... 2.16 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.22 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.21 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161t2.sai ../SRR003161.fastq
[main] Real time: 909.543 sec; CPU: 62.514 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 686.14 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 690.79 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 578.52 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 589.98 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 596.27 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 136.32 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 3407.615 sec; CPU: 3289.492 sec
[bwa_aln_core] convert to sequence coordinate... 6.45 sec
[bwa_aln_core] refine gapped alignments... 2.86 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.74 sec
[bwa_aln_core] refine gapped alignments... 2.63 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.65 sec
[bwa_aln_core] refine gapped alignments... 2.22 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.63 sec
[bwa_aln_core] refine gapped alignments... 1.93 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.44 sec
[bwa_aln_core] refine gapped alignments... 2.00 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.44 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.20 sec
[bwa_aln_core] 1376701 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161t3.sai ../SRR003161.fastq
[main] Real time: 1073.786 sec; CPU: 63.683 sec

结果：

5,bwa aln,31.678,3.930
5,bwa samse,56.784,6.752
250,30.983,3.570
250,49.933,6.212
2500,67.352,9.489
2500,52.633,6.576
25000,96.701,65.804
25000,56.368,6.749
5,31.007,3.347
5,50.984,6.232
250,34.497,3.582
250,52.522,6.290
2500,39.877,9.395
2500,54.645,6.288
25000,95.003,65.583
25000,87.403,6.752
5,32.171,3.414
5,57.861,6.322
250,32.511,3.496
250,55.078,42.617,9.430
2500,112.531,6.439
25000,104.038,65.953
25000,64.331,6.806
1376701,3361.868,3316.962
1376701,877.768,63.236
1376701,3402.127,3285.255
1376701,909.543,62.514
1376701,3407.615,3289.492
1376701,1073.786,63.683

参考：

【1】?http://www.aspzz.cn/article/52491.htm

【2】?http://blog.csdn.net/shengfeixiang/article/details/8820673

【3】?http://vdisk.weibo.com/s/BMqHzrpJg-u-g

【4】?http://www.cnblogs.com/panjun-Donet/archive/2008/07/17/1245472.html