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 testimport scala.io.Sourceimport java.io.File._import java.io.PrintWriterimport scala.collection.mutable.ArrayBufferobject 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[^\:]+)\:""".rval pattern3="""\[bsw2_aln\]\s*read\s*([0-9]+)\s+sequences""".rval 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.toArrayvar 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,120.16066666666667,6.938333333333333,3250,bwa bwasw,477.5166666666667,11.778333333333334,32500,bwa bwasw,2096.4809999999998,40.391,325000,bwa bwasw,3436.9979999999996,213.49533333333332,31376701,bwa bwasw,72196.10933333334,10070.764000000001,35,120.16066666666667,6.938333333333333,3250,477.5166666666667,11.778333333333334,32500,2096.4809999999998,40.391,325000,3436.9979999999996,213.49533333333332,31376701,72196.10933333334,10070.764000000001,3

文件1：

reads,name,RealTime,CPUTime,number5,bwa bwasw,120.16066666666667,6.938333333333333,3250,bwa bwasw,477.5166666666667,11.778333333333334,32500,bwa bwasw,2096.4809999999998,40.391,325000,bwa bwasw,3436.9979999999996,213.49533333333332,31376701,bwa bwasw,72196.10933333334,10070.764000000001,3

文件2：

reads,RealTime,CPUTime,number5,120.16066666666667,6.938333333333333,3250,477.5166666666667,11.778333333333334,32500,2096.4809999999998,40.391,325000,3436.9979999999996,213.49533333333332,31376701,72196.10933333334,10070.764000000001,3