SparkBWA Alignment 분석 도구 설치 및 실행 방법

설치 방법

git clone https://github.com/citiususc/SparkBWA.git
cd SparkBWA

 

~/SparkBWA/src/main/native/Makefile.common 파일 수정

CFLAGS = -g -Wall -Wno-unused-function -O2 -fPIC (변경 또는 추가)
mvn package

 

[실행 명령어]

spark-submit --class SparkBWA --master yarn-client \
   --conf "spark.executor.extraJavaOptions=-Djava.library.path=./bwa.zip" \
   --conf "spark.yarn.executor.memoryOverhead=8704" \
   --driver-memory 4G --executor-memory 8G \
   --executor-cores 1 --archives /BiO/hadoop/program/hadoop_tools/SparkBWA/bwa.zip \
   --num-executors 320 \
   --files /BiO/hadoop/program/hadoop_tools/SparkBWA/log4j.properties \
   /BiO/hadoop/program/hadoop_tools/SparkBWA/SparkBWA.jar -algorithm mem -reads paired -r \
   --index /cache/express/kobic_public/bwa_index/hg19/output.fa  \
   -partitions 320 \
   /user/hadoop/SparkBWA/ERR000589_1.filt.fastq /user/hadoop/SparkBWA/ERR000589_2.filt.fastq  \
   /workspace/spark_bwa/output_test