基因数据处理122之SSW和SparkSW评分不一致，query为Q9_queuedthreadpool 4 threads could not be stopped-CSDN博客

本文链接：https://blog.csdn.net/xubo245/article/details/80589871

本文介绍了一种使用SparkSW和SSW工具进行基因数据比对的实验过程。实验通过不同的参数设置对比了两种工具的性能，并记录了比对结果及耗时情况。涉及的基因数据包括多个序列文件。

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基因数据处理系列

1.解释

RT,但是顺序一致

2.代码：

hadoop@Master:~/disk2/xubo/project/alignment/SparkSW/SparkSW20161114/alluxio-1.3.0$ vi sparkSWSSWQ10.sh 

dir=$(ls -l query/* |awk '!/^d/ {print $NF}' |grep -i '/[9-9]' )
for i in 1 2 3 4 5 6 7 8 9 10
do
echo 'SparkSW:'
#for j in 1 2 3 4 5 6 7 8 9 10
for j in 1 2 3
do
        echo 'time:'$j
        y='/xubo/project/SparkSW/input/D'$i'Line.fasta'
        for file in $dir
         do
                sh test.sh 8G /xubo/project/SparkSW/hash50.csv $file $y 128 1 5
        done
done

echo 'SSW'
#for j in 1 2 3 4 5 6 7 8 9 10
for j in 1 2 3
do

        echo 'time:'$j

        y2='/xubo/project/SparkSW/input/D'$i'Line.fasta'
        #y2='alluxio://Master:19998/xubo/project/SparkSW/input/D'$i'Line.fasta'
         for file in $dir
         do
                sh testSSW.sh 8G /xubo/project/SparkSW/hash50.csv $file $y2 128 1 5
        done
done
done

3.结果：

hadoop@Master:~/disk2/xubo/project/alignment/SparkSW/SparkSW20161114/alluxio-1.3.0$ tail -f sparkSWSSWQ10time201611271348.txt 
SparkSW:
time:1
(9363,UniRef100_A1CLY8)                                                         
time:2
(9363,UniRef100_A1CLY8)                                                         
time:3
(268435464,UniRef100_Q5AWI5)                                                     
(9363,UniRef100_A1CLY8)
SSW
time:1
(9588,UniRef100_A1CLY8)                                                         
time:2
(9588,UniRef100_A1CLY8)                                                         
time:3
(9588,UniRef100_A1CLY8)                                                         
16/11/27 14:45:28 WARN QueuedThreadPool: 3 threads could not be stopped
SparkSW:
time:1
(9363,UniRef100_A1CLY8)                                                         
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
time:2
(9363,UniRef100_A1CLY8)                                                         
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
time:3
(9363,UniRef100_A1CLY8)                                                         
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
SSW
time:1
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
time:2
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
time:3
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
SparkSW:
time:1
(268435461,UniRef100_B1YQQ1)                                                    
(9363,UniRef100_A1CLY8)
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
(6660,UniRef100_Q4WAZ9)
time:2
(268435455,UniRef100_Q48ME3)                                                    
(9363,UniRef100_A1CLY8)
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
(6660,UniRef100_Q4WAZ9)
time:3
(9363,UniRef100_A1CLY8)                                                         
(7756,UniRef100_S0EEY3)
(7695,UniRef100_W7MLD7)
(6660,UniRef100_Q4WAZ9)
(5404,UniRef100_Q0C8M3)
SSW
time:1
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
(6905,UniRef100_Q4WAZ9)
(5620,UniRef100_Q0C8M3)
time:2
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
(6905,UniRef100_Q4WAZ9)
(5620,UniRef100_Q0C8M3)
time:3
(9588,UniRef100_A1CLY8)                                                         
(8014,UniRef100_S0EEY3)
(7958,UniRef100_W7MLD7)
(6905,UniRef100_Q4WAZ9)
(5620,UniRef100_Q0C8M3)

参考

【1】https://github.com/xubo245
【2】http://blog.csdn.net/xubo245/