基因数据处理16之scala对BWASW运行结果进行时间统计

说明：

环境如上篇

对BWASW数据处理的时候pattern需要修改，由于有很多这样的段：

[bsw2_aln] read 17598 sequences/pairs (10000016 bp) ...
[bsw2_aln] read 17644 sequences/pairs (10000056 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10001068 bp) ...
[bsw2_aln] read 17660 sequences/pairs (10001404 bp) ...需要进行第二次pattern，将其进行求和

另外将pattern结果和total结果写在一段代码中，写入两个文件

代码：

package test
import scala.io.Source
import java.io.File._
import java.io.PrintWriter
import scala.collection.mutable.ArrayBuffer
object logPatternBwaswAll extends App {
val directory="file/allbwasw"
//val directory0="file/bwaResult"

val filename=directory+"result/allbwasw.txt"
val filename2=directory+"result/allbwaswTotal.txt"
val out=new PrintWriter(filename)
val out2=new PrintWriter(filename2)
val files = (new java.io.File(directory)).listFiles()
for (ifile <- files) {
val source = Source.fromFile(ifile).mkString
val pattern = """(bwa bwasw)[^\:]+\:\s*([0-9]*.[0-9]*)[^\:]+\:\s*([0-9]*.[0-9]*)""".r
val pattern2="""(\[bsw2_aln\]\s*read\s*[0-9]+\s+sequences[^\:]+)\:""".r
val pattern3="""\[bsw2_aln\]\s*read\s*([0-9]+)\s+sequences""".r

val b1=for(pattern(s1,num1,num2)<-pattern.findAllIn(source)) yield (s1,num1,num2)
val b2=for(pattern2(seq)<-pattern2.findAllIn(source)) yield (seq)
val b22=b2.toArray
var b3=new ArrayBuffer[String]()
//println(b2.length+" "+b22.length);
for(i<-0 until b22.length){
var sump3=0;
for (pattern3(num) <- pattern3.findAllIn(b22(i))) {
sump3=sump3+num.toInt;
}
b3.insert(i, sump3.toString())
}

val b11=b1.toArray
//val b222=b3.toArray
// println("b11.length:"+b11.length+" b3.length:"+b3.length+" b222.length:"+b222.length)

val reads=b3.distinct
// var array2=new ArrayBuffer[ArrayBuffer[String]](reads.length,4)
var array2=Array.ofDim[String](reads.length, 5)

var readsi=0
var arr1=0.0
var arr2=0.0
for(k<-0 until b11.length) {
println(b3(k)+","+b11(k)._1+","+b11(k)._2+","+b11(k)._3)
out.println(b3(k)+","+b11(k)._1+","+b11(k)._2+","+b11(k)._3)
}
for(j<-0 until reads.length){
for(k<-0 until b11.length) {
if(reads(j)==b3(k))
array2(j)(0)=reads(j)
array2(j)(1)=b11(k)._1
array2(j)(2)=(b11(k)._2.toDouble+array2(j)(2).toDouble).toString
array2(j)(3)=(b11(k)._3.toDouble+array2(j)(3).toDouble).toString
array2(j)(3)=(array2(j)(3).toInt+1).toString
}

}
}
out.close()

}

文件：
hadoop@Mcnode2:~/cloud/adam/xubo/data/test20160310/bwasw$ ./bwasw.sh
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 5 sequences/pairs (2691 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 112.694 sec; CPU: 6.378 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 250 sequences/pairs (161179 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 485.574 sec; CPU: 12.060 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 2500 sequences/pairs (1499370 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 2127.204 sec; CPU: 40.981 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 3489.448 sec; CPU: 214.049 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 5 sequences/pairs (2691 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 132.476 sec; CPU: 7.228 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 250 sequences/pairs (161179 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 520.267 sec; CPU: 11.940 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 2500 sequences/pairs (1499370 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 1972.161 sec; CPU: 39.276 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 3474.798 sec; CPU: 213.719 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 5 sequences/pairs (2691 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq
[main] Real time: 115.312 sec; CPU: 7.209 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 250 sequences/pairs (161179 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h1000.fastq
[main] Real time: 426.709 sec; CPU: 11.335 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 2500 sequences/pairs (1499370 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h10000.fastq
[main] Real time: 2190.078 sec; CPU: 40.916 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 7960 sequences/pairs (4469697 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h100000.fastq
[main] Real time: 3346.748 sec; CPU: 212.718 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 17736 sequences/pairs (10000450 bp) ...
[bsw2_aln] read 17632 sequences/pairs (10000617 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000016 bp) ...
[bsw2_aln] read 17644 sequences/pairs (10000056 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10001068 bp) ...
[bsw2_aln] read 17660 sequences/pairs (10001404 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000239 bp) ...
[bsw2_aln] read 17756 sequences/pairs (10000562 bp) ...
[bsw2_aln] read 17168 sequences/pairs (10000899 bp) ...
[bsw2_aln] read 17230 sequences/pairs (10000389 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10001160 bp) ...
[bsw2_aln] read 17684 sequences/pairs (10000797 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10000303 bp) ...
[bsw2_aln] read 17772 sequences/pairs (10000460 bp) ...
[bsw2_aln] read 17722 sequences/pairs (10000941 bp) ...
[bsw2_aln] read 17670 sequences/pairs (10000403 bp) ...
[bsw2_aln] read 17692 sequences/pairs (10000495 bp) ...
[bsw2_aln] read 17732 sequences/pairs (10000515 bp) ...
[bsw2_aln] read 17268 sequences/pairs (10000233 bp) ...
[bsw2_aln] read 16986 sequences/pairs (10001479 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000021 bp) ...
[bsw2_aln] read 17592 sequences/pairs (10001063 bp) ...
[bsw2_aln] read 17608 sequences/pairs (10000532 bp) ...
[bsw2_aln] read 17634 sequences/pairs (10000966 bp) ...
[bsw2_aln] read 17610 sequences/pairs (10000375 bp) ...
[bsw2_aln] read 17630 sequences/pairs (10000393 bp) ...
[bsw2_aln] read 17688 sequences/pairs (10001395 bp) ...
[bsw2_aln] read 17672 sequences/pairs (10000206 bp) ...
[bsw2_aln] read 17246 sequences/pairs (10000227 bp) ...
[bsw2_aln] read 16678 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 16782 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000968 bp) ...
[bsw2_aln] read 17358 sequences/pairs (10000936 bp) ...
[bsw2_aln] read 17578 sequences/pairs (10000630 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000372 bp) ...
[bsw2_aln] read 17478 sequences/pairs (10000575 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10001079 bp) ...
[bsw2_aln] read 17424 sequences/pairs (10002025 bp) ...
[bsw2_aln] read 16508 sequences/pairs (10000430 bp) ...
[bsw2_aln] read 17426 sequences/pairs (10001030 bp) ...
[bsw2_aln] read 17766 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 17664 sequences/pairs (10001067 bp) ...
[bsw2_aln] read 17482 sequences/pairs (10000317 bp) ...
[bsw2_aln] read 17564 sequences/pairs (10000063 bp) ...
[bsw2_aln] read 17446 sequences/pairs (10000263 bp) ...
[bsw2_aln] read 17466 sequences/pairs (10000042 bp) ...
[bsw2_aln] read 17566 sequences/pairs (10000825 bp) ...
[bsw2_aln] read 17366 sequences/pairs (10000771 bp) ...
[bsw2_aln] read 17296 sequences/pairs (10001904 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10000280 bp) ...
[bsw2_aln] read 17648 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000390 bp) ...
[bsw2_aln] read 17562 sequences/pairs (10000598 bp) ...
[bsw2_aln] read 17576 sequences/pairs (10000441 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000038 bp) ...
[bsw2_aln] read 17558 sequences/pairs (10001083 bp) ...
[bsw2_aln] read 17486 sequences/pairs (10000213 bp) ...
[bsw2_aln] read 17428 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000565 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000634 bp) ...
[bsw2_aln] read 17554 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17544 sequences/pairs (10000358 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000017 bp) ...
[bsw2_aln] read 17452 sequences/pairs (10000587 bp) ...
[bsw2_aln] read 17522 sequences/pairs (10000559 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10001210 bp) ...
[bsw2_aln] read 17406 sequences/pairs (10000246 bp) ...
[bsw2_aln] read 17394 sequences/pairs (10000655 bp) ...
[bsw2_aln] read 17132 sequences/pairs (10000531 bp) ...
[bsw2_aln] read 17070 sequences/pairs (10000705 bp) ...
[bsw2_aln] read 17280 sequences/pairs (10000702 bp) ...
[bsw2_aln] read 17504 sequences/pairs (10000584 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10000908 bp) ...
[bsw2_aln] read 17484 sequences/pairs (10000456 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10000394 bp) ...
[bsw2_aln] read 17324 sequences/pairs (10000472 bp) ...
[bsw2_aln] read 17152 sequences/pairs (10000658 bp) ...
[bsw2_aln] read 14281 sequences/pairs (8410932 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 73953.156 sec; CPU: 10089.564 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 17736 sequences/pairs (10000450 bp) ...
[bsw2_aln] read 17632 sequences/pairs (10000617 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000016 bp) ...
[bsw2_aln] read 17644 sequences/pairs (10000056 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10001068 bp) ...
[bsw2_aln] read 17660 sequences/pairs (10001404 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000239 bp) ...
[bsw2_aln] read 17756 sequences/pairs (10000562 bp) ...
[bsw2_aln] read 17168 sequences/pairs (10000899 bp) ...
[bsw2_aln] read 17230 sequences/pairs (10000389 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10001160 bp) ...
[bsw2_aln] read 17684 sequences/pairs (10000797 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10000303 bp) ...
[bsw2_aln] read 17772 sequences/pairs (10000460 bp) ...
[bsw2_aln] read 17722 sequences/pairs (10000941 bp) ...
[bsw2_aln] read 17670 sequences/pairs (10000403 bp) ...
[bsw2_aln] read 17692 sequences/pairs (10000495 bp) ...
[bsw2_aln] read 17732 sequences/pairs (10000515 bp) ...
[bsw2_aln] read 17268 sequences/pairs (10000233 bp) ...
[bsw2_aln] read 16986 sequences/pairs (10001479 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000021 bp) ...
[bsw2_aln] read 17592 sequences/pairs (10001063 bp) ...
[bsw2_aln] read 17608 sequences/pairs (10000532 bp) ...
[bsw2_aln] read 17634 sequences/pairs (10000966 bp) ...
[bsw2_aln] read 17610 sequences/pairs (10000375 bp) ...
[bsw2_aln] read 17630 sequences/pairs (10000393 bp) ...
[bsw2_aln] read 17688 sequences/pairs (10001395 bp) ...
[bsw2_aln] read 17672 sequences/pairs (10000206 bp) ...
[bsw2_aln] read 17246 sequences/pairs (10000227 bp) ...
[bsw2_aln] read 16678 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 16782 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000968 bp) ...
[bsw2_aln] read 17358 sequences/pairs (10000936 bp) ...
[bsw2_aln] read 17578 sequences/pairs (10000630 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000372 bp) ...
[bsw2_aln] read 17478 sequences/pairs (10000575 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10001079 bp) ...
[bsw2_aln] read 17424 sequences/pairs (10002025 bp) ...
[bsw2_aln] read 16508 sequences/pairs (10000430 bp) ...
[bsw2_aln] read 17426 sequences/pairs (10001030 bp) ...
[bsw2_aln] read 17766 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 17664 sequences/pairs (10001067 bp) ...
[bsw2_aln] read 17482 sequences/pairs (10000317 bp) ...
[bsw2_aln] read 17564 sequences/pairs (10000063 bp) ...
[bsw2_aln] read 17446 sequences/pairs (10000263 bp) ...
[bsw2_aln] read 17466 sequences/pairs (10000042 bp) ...
[bsw2_aln] read 17566 sequences/pairs (10000825 bp) ...
[bsw2_aln] read 17366 sequences/pairs (10000771 bp) ...
[bsw2_aln] read 17296 sequences/pairs (10001904 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10000280 bp) ...
[bsw2_aln] read 17648 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000390 bp) ...
[bsw2_aln] read 17562 sequences/pairs (10000598 bp) ...
[bsw2_aln] read 17576 sequences/pairs (10000441 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000038 bp) ...
[bsw2_aln] read 17558 sequences/pairs (10001083 bp) ...
[bsw2_aln] read 17486 sequences/pairs (10000213 bp) ...
[bsw2_aln] read 17428 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000565 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000634 bp) ...
[bsw2_aln] read 17554 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17544 sequences/pairs (10000358 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000017 bp) ...
[bsw2_aln] read 17452 sequences/pairs (10000587 bp) ...
[bsw2_aln] read 17522 sequences/pairs (10000559 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10001210 bp) ...
[bsw2_aln] read 17406 sequences/pairs (10000246 bp) ...
[bsw2_aln] read 17394 sequences/pairs (10000655 bp) ...
[bsw2_aln] read 17132 sequences/pairs (10000531 bp) ...
[bsw2_aln] read 17070 sequences/pairs (10000705 bp) ...
[bsw2_aln] read 17280 sequences/pairs (10000702 bp) ...
[bsw2_aln] read 17504 sequences/pairs (10000584 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10000908 bp) ...
[bsw2_aln] read 17484 sequences/pairs (10000456 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10000394 bp) ...
[bsw2_aln] read 17324 sequences/pairs (10000472 bp) ...
[bsw2_aln] read 17152 sequences/pairs (10000658 bp) ...
[bsw2_aln] read 14281 sequences/pairs (8410932 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 72603.284 sec; CPU: 10059.902 sec
[M::bwa_idx_load_from_disk] read 261 ALT contigs
[bsw2_aln] read 17040 sequences/pairs (10000385 bp) ...
[bsw2_aln] read 17736 sequences/pairs (10000450 bp) ...
[bsw2_aln] read 17632 sequences/pairs (10000617 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000016 bp) ...
[bsw2_aln] read 17644 sequences/pairs (10000056 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10001068 bp) ...
[bsw2_aln] read 17660 sequences/pairs (10001404 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000239 bp) ...
[bsw2_aln] read 17756 sequences/pairs (10000562 bp) ...
[bsw2_aln] read 17168 sequences/pairs (10000899 bp) ...
[bsw2_aln] read 17230 sequences/pairs (10000389 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10001160 bp) ...
[bsw2_aln] read 17684 sequences/pairs (10000797 bp) ...
[bsw2_aln] read 17668 sequences/pairs (10000303 bp) ...
[bsw2_aln] read 17772 sequences/pairs (10000460 bp) ...
[bsw2_aln] read 17722 sequences/pairs (10000941 bp) ...
[bsw2_aln] read 17670 sequences/pairs (10000403 bp) ...
[bsw2_aln] read 17692 sequences/pairs (10000495 bp) ...
[bsw2_aln] read 17732 sequences/pairs (10000515 bp) ...
[bsw2_aln] read 17268 sequences/pairs (10000233 bp) ...
[bsw2_aln] read 16986 sequences/pairs (10001479 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000021 bp) ...
[bsw2_aln] read 17592 sequences/pairs (10001063 bp) ...
[bsw2_aln] read 17608 sequences/pairs (10000532 bp) ...
[bsw2_aln] read 17634 sequences/pairs (10000966 bp) ...
[bsw2_aln] read 17610 sequences/pairs (10000375 bp) ...
[bsw2_aln] read 17630 sequences/pairs (10000393 bp) ...
[bsw2_aln] read 17688 sequences/pairs (10001395 bp) ...
[bsw2_aln] read 17672 sequences/pairs (10000206 bp) ...
[bsw2_aln] read 17246 sequences/pairs (10000227 bp) ...
[bsw2_aln] read 16678 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 16782 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000968 bp) ...
[bsw2_aln] read 17358 sequences/pairs (10000936 bp) ...
[bsw2_aln] read 17578 sequences/pairs (10000630 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000372 bp) ...
[bsw2_aln] read 17478 sequences/pairs (10000575 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10001079 bp) ...
[bsw2_aln] read 17424 sequences/pairs (10002025 bp) ...
[bsw2_aln] read 16508 sequences/pairs (10000430 bp) ...
[bsw2_aln] read 17426 sequences/pairs (10001030 bp) ...
[bsw2_aln] read 17766 sequences/pairs (10000476 bp) ...
[bsw2_aln] read 17664 sequences/pairs (10001067 bp) ...
[bsw2_aln] read 17482 sequences/pairs (10000317 bp) ...
[bsw2_aln] read 17564 sequences/pairs (10000063 bp) ...
[bsw2_aln] read 17446 sequences/pairs (10000263 bp) ...
[bsw2_aln] read 17466 sequences/pairs (10000042 bp) ...
[bsw2_aln] read 17566 sequences/pairs (10000825 bp) ...
[bsw2_aln] read 17366 sequences/pairs (10000771 bp) ...
[bsw2_aln] read 17296 sequences/pairs (10001904 bp) ...
[bsw2_aln] read 17650 sequences/pairs (10000280 bp) ...
[bsw2_aln] read 17648 sequences/pairs (10000709 bp) ...
[bsw2_aln] read 17658 sequences/pairs (10000390 bp) ...
[bsw2_aln] read 17562 sequences/pairs (10000598 bp) ...
[bsw2_aln] read 17576 sequences/pairs (10000441 bp) ...
[bsw2_aln] read 17598 sequences/pairs (10000038 bp) ...
[bsw2_aln] read 17558 sequences/pairs (10001083 bp) ...
[bsw2_aln] read 17486 sequences/pairs (10000213 bp) ...
[bsw2_aln] read 17428 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17316 sequences/pairs (10000565 bp) ...
[bsw2_aln] read 17376 sequences/pairs (10000634 bp) ...
[bsw2_aln] read 17554 sequences/pairs (10000555 bp) ...
[bsw2_aln] read 17544 sequences/pairs (10000358 bp) ...
[bsw2_aln] read 17546 sequences/pairs (10000017 bp) ...
[bsw2_aln] read 17452 sequences/pairs (10000587 bp) ...
[bsw2_aln] read 17522 sequences/pairs (10000559 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10001210 bp) ...
[bsw2_aln] read 17406 sequences/pairs (10000246 bp) ...
[bsw2_aln] read 17394 sequences/pairs (10000655 bp) ...
[bsw2_aln] read 17132 sequences/pairs (10000531 bp) ...
[bsw2_aln] read 17070 sequences/pairs (10000705 bp) ...
[bsw2_aln] read 17280 sequences/pairs (10000702 bp) ...
[bsw2_aln] read 17504 sequences/pairs (10000584 bp) ...
[bsw2_aln] read 17480 sequences/pairs (10000908 bp) ...
[bsw2_aln] read 17484 sequences/pairs (10000456 bp) ...
[bsw2_aln] read 17420 sequences/pairs (10000394 bp) ...
[bsw2_aln] read 17324 sequences/pairs (10000472 bp) ...
[bsw2_aln] read 17152 sequences/pairs (10000658 bp) ...
[bsw2_aln] read 14281 sequences/pairs (8410932 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161.fastq
[main] Real time: 70031.888 sec; CPU: 10062.826 sec


运行结果：
5,bwa bwasw,120.16066666666667,6.938333333333333,3
250,bwa bwasw,477.5166666666667,11.778333333333334,3
2500,bwa bwasw,2096.4809999999998,40.391,3
25000,bwa bwasw,3436.9979999999996,213.49533333333332,3
1376701,bwa bwasw,72196.10933333334,10070.764000000001,3
5,120.16066666666667,6.938333333333333,3
250,477.5166666666667,11.778333333333334,3
2500,2096.4809999999998,40.391,3
25000,3436.9979999999996,213.49533333333332,3
1376701,72196.10933333334,10070.764000000001,3
文件1：
reads,name,RealTime,CPUTime,number
5,bwa bwasw,120.16066666666667,6.938333333333333,3
250,bwa bwasw,477.5166666666667,11.778333333333334,3
2500,bwa bwasw,2096.4809999999998,40.391,3
25000,bwa bwasw,3436.9979999999996,213.49533333333332,3
1376701,bwa bwasw,72196.10933333334,10070.764000000001,3


文件2：
reads,RealTime,CPUTime,number
5,120.16066666666667,6.938333333333333,3
250,477.5166666666667,11.778333333333334,3
2500,2096.4809999999998,40.391,3
25000,3436.9979999999996,213.49533333333332,3
1376701,72196.10933333334,10070.764000000001,3