基因数据处理103之SparkBWAYarn模式运行100万条paired-reads实例

脚本:

spark-submit --class SparkBWA \
--master yarn-client \
--conf "spark.executor.extraJavaOptions=-Djava.library.path=/home/hadoop/xubo/tools/SparkBWA/build" \
--archives ./bwa.zip \
SparkBWA.jar \
-algorithm mem -reads paired \
-index /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta \
-partitions 3 \
/xubo/alignment/sparkBWA/GRCH38chr1L3556522N1000000L100paired1.fastq /xubo/alignment/sparkBWA/GRCH38chr1L3556522N1000000L100paired2.fastq \
/xubo/alignment/output/sparkBWA/GRCH38chr1L3556522N1000000L100paired12Yarn

运行脚本记录:

hadoop@Master:~/xubo/tools/SparkBWA/build$ ./pairedGRCH38L1N1000000Yarn.sh 
hadoop@Master:~/xubo/tools/SparkBWA/build$  

本地和yarn比较:

App ID  App Name    Started Completed ▾ Duration    Spark User  Last Updated
application_1466433907244_0149  SparkBWA_GRCH38chr1L3556522N1000000L100paired1.fastq-3-NoSort   2016/06/24 19:02:26     2016/06/24 19:13:26     11 min  hadoop  2016/06/24 19:13:26
application_1466433907244_0148  SparkBWA_GRCH38chr1L3556522N10L50paired1.fastq-3-NoSort     2016/06/24 18:59:28     2016/06/24 19:00:07     39 s    hadoop  2016/06/24 19:00:07
application_1466433907244_0147  SparkBWA_GRCH38chr1L3556522N10L50paired1.fastq-3-NoSort     2016/06/24 18:55:04     2016/06/24 18:56:54     1.8 min     hadoop  2016/06/24 18:56:54
application_1466433907244_0145  SparkBWA_GRCH38chr1L3556522N10L50paired1.fastq-3-NoSort     2016/06/24 18:46:51     2016/06/24 18:47:51     1.0 min     hadoop  2016/06/24 18:47:51
application_1466433907244_0143  SparkBWA_GRCH38chr1L3556522N10L50paired1.fastq-3-NoSort     2016/06/24 18:33:20     2016/06/24 18:35:07     1.8 min     hadoop  2016/06/24 18:35:07
local-1466761536651 SparkBWA_GRCH38chr1L3556522N1000000L100paired1.fastq-3-NoSort   2016/06/24 17:45:34     2016/06/24 18:01:46     16 min  hadoop  2016/06/24 18:01:46

local模式是16min
yarn模式是11min

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
【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  
【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

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
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