基因数据处理53之cs-bwamem集群版运行paird-end（1千万条100bp的reads）

art：

art_illumina -ss HS20 -i GRCH38BWAindex/GRCH38chr1L3556522.fna -p -l 100 -m 200 -s 10  -c 10000000 -o g38L100c10000000Nhs20Paired

2.fastq上传到hdfs

spark-submit  --class cs.ucla.edu.bwaspark.BWAMEMSpark --master spark://219.219.220.149:7077  /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar upload-fastq   1 21 g38L100c10000000Nhs20Paired1.fq g38L100c10000000Nhs20Paired2.fq /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12.fastq

3.配置：

需要将fasta dispatch到各个节点，每个节点需要有cs-bwamem的jar包，jni搞全局路径

4.align：

spark-submit --executor-memory 4g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 20 --master spark://219.219.220.149:7077  --conf spark.driver.host=219.219.220.149 --conf spark.driver.cores=4 --conf spark.driver.maxResultSize=4g --conf spark.storage.memoryFraction=0.7  --conf spark.akka.threads=2 --conf spark.akka.frameSize=1024 /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar cs-bwamem -bfn 1 -bPSW 1 -sbatch 10 -bPSWJNI 1  -oChoice 2 -oPath hdfs://219.219.220.149:9000/xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12F2.adam -localRef 1 -jniPath /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/jniNative.so -isSWExtBatched 1  1 /home/hadoop/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem/GRCH38BWAindex/GRCH38chr1L3556522.fasta  /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12.fastq

5.merge：

spark-submit --executor-memory 6g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 20 --master spark://219.219.220.149:7077  --conf spark.driver.host=219.219.220.149 --conf spark.driver.cores=4 --conf spark.driver.maxResultSize=6g --conf spark.storage.memoryFraction=0.7  --conf spark.akka.threads=2 --conf spark.akka.frameSize=1024 /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0-assembly.jar merge hdfs://219.219.220.149:9000 /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12F2.adam /xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12F2.merge.adam

6.统计：

package org.bdgenomics.avocado.cli

import org.apache.spark.sql.SQLContext
import org.apache.spark.{SparkConf, SparkContext}

/**
* Created by xubo on 2016/5/27.
* 从hdfs下载经过avocado匹配好的数据
* run:success
*/
object parquetRead2csbwamemDup {
def main(args: Array[String]) {
val conf = new SparkConf().setMaster("local[4]").setAppName(this.getClass().getSimpleName().filter(!_.equals('$')))
val sc = new SparkContext(conf)
val sqlContext = new SQLContext(sc)
println("start:")
//    val file = "hdfs://219.219.220.149:9000/xubo/16.adam/0"
//    val file = "hdfs://219.219.220.149:9000/xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20.merge.adam/"
val file = "hdfs://219.219.220.149:9000/xubo/data/alignment/cs-bwamem/fastq/g38L100c10000000Nhs20Paired12F2.merge.adam/"

val df3 = sqlContext.read.option("mergeSchema", "true").parquet(file)
//    df3.printSchema()
df3.show()
println(df3.count())
var j = 1
//    for (i <- df3) {
//      println(j + ":" + i)
//      j += 1
//    }
//    println("distinct:" + df3.distinct.count())
sc.stop
println("end")
}
}

结果：

scala>     println(df3.count())
18512773
scala> println("distinct:" + df3.distinct.count())
distinct:18512773

附录：

部分记录：

analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.56094168004282, 9.939863106970265)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.56094168004282 9.939863106970265
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.3929171883384, 9.895888368589208)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.3929171883384 9.895888368589208
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5008221332571, 9.893101752855983)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5008221332571 9.893101752855983
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.50341742708892, 9.938821490084942)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.50341742708892 9.938821490084942
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.43662172257996, 9.956950171714343)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.43662172257996 9.956950171714343
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5294684266857, 9.903683785238687)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5294684266857 9.903683785238687
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.40190347187567, 9.937420104198324)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.40190347187567 9.937420104198324
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.45073240443014, 10.004935473704805)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.45073240443014 10.004935473704805
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.48925135028793, 9.872713569624056)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.48925135028793 9.872713569624056
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.40273561658512, 9.90951049687331)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.40273561658512 9.90951049687331
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.46782169411932, 9.994092930915187)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.46782169411932 9.994092930915187
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4832529043789, 9.916498387414416)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4832529043789 9.916498387414416
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.51942615912995, 9.980650734352077)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.51942615912995 9.980650734352077
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.42283366088975, 10.025277342223173)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.42283366088975 10.025277342223173
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.56863795443184, 9.884954572476323)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.56863795443184 9.884954572476323
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.54418222714128, 9.937606729429495)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.54418222714128 9.937606729429495
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.51789788933257, 9.908230182966792)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.51789788933257 9.908230182966792
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.49175824175825, 9.953633581247528)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.49175824175825 9.953633581247528
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.57901688501767, 9.95075215935561)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.57901688501767 9.95075215935561
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.47238496713348, 9.984373782742304)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.47238496713348 9.984373782742304
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.46635524016688, 9.968761617488683)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.46635524016688 9.968761617488683
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.38825547732228, 9.92027510738216)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.38825547732228 9.92027510738216
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4851967207246, 9.937352774317741)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4851967207246 9.937352774317741
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.55340706386016, 9.817553555623133)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.55340706386016 9.817553555623133
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.44619450694668, 9.920089825716484)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.44619450694668 9.920089825716484
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5452329749104, 9.926594228354224)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5452329749104 9.926594228354224
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.45703727621714, 9.948262102053539)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.45703727621714 9.948262102053539
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4996774887121, 9.889445679734042)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4996774887121 9.889445679734042
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.44845544695727, 10.04637179033811)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.44845544695727 10.04637179033811
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.54115079081086, 9.861927310088358)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.54115079081086 9.861927310088358
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.50392688847637, 9.923422645866905)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.50392688847637 9.923422645866905
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.47992413398225, 9.938359869833343)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.47992413398225 9.938359869833343
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.58786034019695, 9.881771439959131)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.58786034019695 9.881771439959131
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.53944973771544, 9.928751173123029)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.53944973771544 9.928751173123029
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.51932833154697, 9.921047819212657)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.51932833154697 9.921047819212657
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5051575828961, 9.955724349633446)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5051575828961 9.955724349633446
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.45987665323875, 9.934862525129335)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.45987665323875 9.934862525129335
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.41697601370646, 9.924344174968864)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.41697601370646 9.924344174968864
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4504008016032, 10.037075657682921)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4504008016032 10.037075657682921
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.53644939965696, 9.99170757810556)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.53644939965696 9.99170757810556
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.48251923421006, 9.977411795227688)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.48251923421006 9.977411795227688
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.50750643408637, 9.996386292381906)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.50750643408637 9.996386292381906
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.43163108941235, 9.93712833366825)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.43163108941235 9.93712833366825
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4462753788962, 9.969547663168125)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4462753788962 9.969547663168125
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.564805511698, 9.981653834837397)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.564805511698 9.981653834837397
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.36601983305985, 9.935551164661065)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.36601983305985 9.935551164661065
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5214522629195, 9.948307577425197)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5214522629195 9.948307577425197
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.4983700519434, 9.945836975580079)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.4983700519434 9.945836975580079
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.55142989753293, 9.949033183252514)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.55142989753293 9.949033183252514
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.57046907934694, 9.951195165671601)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.57046907934694 9.951195165671601
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5627628483855, 9.940990579395123)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5627628483855 9.940990579395123
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.57557661362418, 9.88907098626934)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.57557661362418 9.88907098626934
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.43170531280145, 9.97153529406552)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.43170531280145 9.97153529406552
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.50119476443524, 9.993324406109274)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.50119476443524 9.993324406109274
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.53636818766986, 9.949249012517377)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.53636818766986 9.949249012517377
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.56565548290277, 9.982952754471368)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.56565548290277 9.982952754471368
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.44116064703562, 9.922618947362455)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.44116064703562 9.922618947362455
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.48944921316166, 9.932084984684073)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.48944921316166 9.932084984684073
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.3957828750534, 9.897098539777856)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.3957828750534 9.897098539777856
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.46895465769603, 9.819260659759172)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.46895465769603 9.819260659759172
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.5120634807163, 9.905862404052492)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.5120634807163 9.905862404052492
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.50274353310056, 9.979749125168556)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.50274353310056 9.979749125168556
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.49695820211852, 9.940759507891329)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.49695820211852 9.940759507891329
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.42262032467997, 9.919691202862072)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.42262032467997 9.919691202862072
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.49617638650656, 9.973742669699334)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.49617638650656 9.973742669699334
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.57427937915742, 9.952728233473406)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.57427937915742 9.952728233473406
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 198, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.48755438271164, 9.944608296251676)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.48755438271164 9.944608296251676
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.52546792398914, 10.000808728139058)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.52546792398914 10.000808728139058
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (192, 199, 205)
low and high boundaries for computing mean and std.dev: (166, 231)
mean and std.dev: (198.49446902654867, 9.999977060170599)
low and high boundaries for proper pairs: (153, 244)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 153 244 0 198.49446902654867 9.999977060170599
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Load FASTQ files
@Worker1
skip orientation FF as there are not enough pairs
analyzing insert size distribution for orientation
(25, 50, 75) percentile: (191, 198, 205)
low and high boundaries for computing mean and std.dev: (163, 233)
mean and std.dev: (198.28641975308642, 10.159216233717126)
low and high boundaries for proper pairs: (149, 247)
skip orientation RF as there are not enough pairs
skip orientation RR as there are not enough pairs
@MemPeStat
pes(0): 0 0 1 0.0 0.0
pes(1): 149 247 0 198.28641975308642 10.159216233717126
pes(2): 0 0 1 0.0 0.0
pes(3): 0 0 1 0.0 0.0
Summary:
Worker1 Time: 815792
Calculate Metrics Time: 2093
Worker2 Time: 688463
16/06/03 18:07:19 ERROR LiveListenerBus: SparkListenerBus has already stopped! Dropping event SparkListenerExecutorMetricsUpdate(4,WrappedArray())
16/06/03 18:07:19 WARN QueuedThreadPool: 1 threads could not be stopped
CS-BWAMEM Finished!!!
Jun 3, 2016 5:41:47 PM INFO: parquet.hadoop.ParquetInputFormat: Total input paths to process : 21
Jun 3, 2016 5:41:57 PM INFO: parquet.hadoop.ParquetInputFormat: Total input paths to process : 21
hadoop@Master:~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem$

参考

【1】https://github.com/xubo245/AdamLearning
【2】https://github.com/bigdatagenomics/adam/
【3】https://github.com/xubo245/SparkLearning
【4】http://spark.apache.org

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)
【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).
【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).
【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: xubo245@mail.ustc.edu.cn
Wechat: xu601450868
QQ: 601450868