基因数据处理46之cloud-scale-bwamem安装（compile.pl安装没问题）

版本：https://github.com/ytchen0323/cloud-scale-bwamem/releases/tag/v0.2.1

1.需要设置spark路径：

            
            <systemPath>/home/hadoop/cloud/spark-1.5.2/lib/spark-assembly-1.5.2-hadoop2.6.0.jarsystemPath>

2.需要设置：

sudo mkdir -p  /home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/
 cp target/cloud-scale-bwamem-0.2.0-assembly.jar  /home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/

变异成功：

安装记录：

hadoop@Master:~/xubo/tools/cloud-scale-bwamem-0.2.1$ ./compile.pl 
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:cloud-scale-bwamem:jar:0.2.0
[WARNING] 'dependencies.dependency.systemPath' for org.apache.spark:spark-core_${scala.artifact.suffix}:jar should use a variable instead of a hard-coded path /home/hadoop/cloud/spark-1.5.2/lib/spark-assembly-1.5.2-hadoop2.6.0.jar @ line 246, column 25
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-shade-plugin is missing. @ line 145, column 21
[WARNING] 'build.plugins.plugin.version' for org.scala-tools:maven-scala-plugin is missing. @ line 89, column 21
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Cloud-Scale-BWAMEM 0.2.0
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ cloud-scale-bwamem ---
[INFO] Deleting /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:schema (default) @ cloud-scale-bwamem ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:protocol (default) @ cloud-scale-bwamem ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:idl-protocol (default) @ cloud-scale-bwamem ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ cloud-scale-bwamem ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/resources
[INFO] 
[INFO] --- maven-scala-plugin:2.15.2:compile (default) @ cloud-scale-bwamem ---
[INFO] Checking for multiple versions of scala
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  cs.ucla.edu:cloud-scale-bwamem:0.2.0 requires scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] includes = [**/*.scala,**/*.java,]
[INFO] excludes = []
[INFO] /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/java:-1: info: compiling
[INFO] /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/scala:-1: info: compiling
[INFO] Compiling 77 source files to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/classes at 1464864814805
[WARNING] warning: there were 22 deprecation warning(s); re-run with -deprecation for details
[WARNING] warning: there were 1 feature warning(s); re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 51 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ cloud-scale-bwamem ---
[INFO] Changes detected - recompiling the module!
[WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent!
[INFO] Compiling 8 source files to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/classes
[INFO] 
[INFO] --- maven-scala-plugin:2.15.2:compile (compile) @ cloud-scale-bwamem ---
[INFO] Checking for multiple versions of scala
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  cs.ucla.edu:cloud-scale-bwamem:0.2.0 requires scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] includes = [**/*.scala,**/*.java,]
[INFO] excludes = []
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ cloud-scale-bwamem ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ cloud-scale-bwamem ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-scala-plugin:2.15.2:testCompile (test-compile) @ cloud-scale-bwamem ---
[INFO] Checking for multiple versions of scala
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  cs.ucla.edu:cloud-scale-bwamem:0.2.0 requires scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] includes = [**/*.scala,**/*.java,]
[INFO] excludes = []
[WARNING] No source files found.
[INFO] 
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ cloud-scale-bwamem ---
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ cloud-scale-bwamem ---
[INFO] Building jar: /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/cloud-scale-bwamem-0.2.0.jar
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:copy-dependencies (default) @ cloud-scale-bwamem ---
[INFO] Copying protobuf-java-2.5.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/protobuf-java-2.5.0.jar
[INFO] Copying parquet-jackson-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-jackson-1.4.3.jar
[INFO] Copying jcommander-1.27.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jcommander-1.27.jar
[INFO] Copying api-asn1-api-1.0.0-M20.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/api-asn1-api-1.0.0-M20.jar
[INFO] Copying api-util-1.0.0-M20.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/api-util-1.0.0-M20.jar
[INFO] Copying testng-6.8.8.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/testng-6.8.8.jar
[INFO] Copying xz-1.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/xz-1.0.jar
[INFO] Copying commons-logging-1.1.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-logging-1.1.1.jar
[INFO] Copying kryo-2.21.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/kryo-2.21.jar
[INFO] Copying hadoop-mapreduce-client-app-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-mapreduce-client-app-2.5.2.jar
[INFO] Copying jakarta-regexp-1.4.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jakarta-regexp-1.4.jar
[INFO] Copying commons-lang-2.6.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-lang-2.6.jar
[INFO] Copying ant-1.8.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/ant-1.8.2.jar
[INFO] Copying hadoop-auth-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-auth-2.5.2.jar
[INFO] Copying reflectasm-1.07-shaded.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/reflectasm-1.07-shaded.jar
[INFO] Copying hadoop-yarn-server-common-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-yarn-server-common-2.5.2.jar
[INFO] Copying jersey-core-1.9.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jersey-core-1.9.jar
[INFO] Copying bcel-5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/bcel-5.2.jar
[INFO] Copying jackson-mapper-asl-1.9.13.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jackson-mapper-asl-1.9.13.jar
[INFO] Copying leveldbjni-all-1.8.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/leveldbjni-all-1.8.jar
[INFO] Copying commons-beanutils-1.7.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-beanutils-1.7.0.jar
[INFO] Copying hadoop-bam-7.0.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-bam-7.0.0.jar
[INFO] Copying hadoop-client-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-client-2.5.2.jar
[INFO] Copying jetty-util-6.1.26.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jetty-util-6.1.26.jar
[INFO] Copying ant-launcher-1.8.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/ant-launcher-1.8.2.jar
[INFO] Copying annotations-2.0.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/annotations-2.0.0.jar
[INFO] Copying objenesis-1.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/objenesis-1.2.jar
[INFO] Copying log4j-1.2.17.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/log4j-1.2.17.jar
[INFO] Copying scala-library-2.10.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/scala-library-2.10.3.jar
[INFO] Copying guava-11.0.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/guava-11.0.2.jar
[INFO] Copying commons-httpclient-3.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-httpclient-3.1.jar
[INFO] Copying adam-core-0.14.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/adam-core-0.14.0.jar
[INFO] Copying netty-3.6.2.Final.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/netty-3.6.2.Final.jar
[INFO] Copying parquet-avro-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-avro-1.4.3.jar
[INFO] Copying commons-digester-1.8.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-digester-1.8.jar
[INFO] Copying paranamer-2.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/paranamer-2.3.jar
[INFO] Copying activation-1.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/activation-1.1.jar
[INFO] Copying xmlenc-0.52.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/xmlenc-0.52.jar
[INFO] Copying parquet-generator-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-generator-1.4.3.jar
[INFO] Copying commons-beanutils-core-1.8.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-beanutils-core-1.8.0.jar
[INFO] Copying hadoop-annotations-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-annotations-2.5.2.jar
[INFO] Copying hadoop-mapreduce-client-core-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-mapreduce-client-core-2.5.2.jar
[INFO] Copying servo-core-0.5.5.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/servo-core-0.5.5.jar
[INFO] Copying commons-cli-1.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-cli-1.2.jar
[INFO] Copying commons-io-1.3.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-io-1.3.2.jar
[INFO] Copying apacheds-kerberos-codec-2.0.0-M15.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/apacheds-kerberos-codec-2.0.0-M15.jar
[INFO] Copying stax-api-1.0-2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/stax-api-1.0-2.jar
[INFO] Copying spark-assembly-1.5.2-hadoop2.6.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/spark-core_2.10-1.3.1.jar
[INFO] Copying htsjdk-1.118.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/htsjdk-1.118.jar
[INFO] Copying hadoop-yarn-common-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-yarn-common-2.5.2.jar
[INFO] Copying jsr305-1.3.9.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jsr305-1.3.9.jar
[INFO] Copying zookeeper-3.4.6.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/zookeeper-3.4.6.jar
[INFO] Copying parquet-format-2.0.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-format-2.0.0.jar
[INFO] Copying apacheds-i18n-2.0.0-M15.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/apacheds-i18n-2.0.0-M15.jar
[INFO] Copying jaxb-api-2.2.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jaxb-api-2.2.2.jar
[INFO] Copying snappy-java-1.0.5.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/snappy-java-1.0.5.jar
[INFO] Copying hadoop-mapreduce-client-common-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-mapreduce-client-common-2.5.2.jar
[INFO] Copying parquet-encoding-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-encoding-1.4.3.jar
[INFO] Copying slf4j-api-1.6.4.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/slf4j-api-1.6.4.jar
[INFO] Copying commons-compress-1.4.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-compress-1.4.1.jar
[INFO] Copying hadoop-hdfs-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-hdfs-2.5.2.jar
[INFO] Copying minlog-1.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/minlog-1.2.jar
[INFO] Copying parquet-common-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-common-1.4.3.jar
[INFO] Copying cofoja-1.1-r150.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/cofoja-1.1-r150.jar
[INFO] Copying commons-codec-1.4.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-codec-1.4.jar
[INFO] Copying hadoop-common-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-common-2.5.2.jar
[INFO] Copying commons-collections-3.2.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-collections-3.2.1.jar
[INFO] Copying jersey-client-1.9.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jersey-client-1.9.jar
[INFO] Copying commons-math3-3.1.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-math3-3.1.1.jar
[INFO] Copying parquet-hadoop-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-hadoop-1.4.3.jar
[INFO] Copying hadoop-yarn-client-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-yarn-client-2.5.2.jar
[INFO] Copying slf4j-log4j12-1.7.5.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/slf4j-log4j12-1.7.5.jar
[INFO] Copying fastutil-6.4.4.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/fastutil-6.4.4.jar
[INFO] Copying bsh-2.0b4.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/bsh-2.0b4.jar
[INFO] Copying commons-configuration-1.6.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-configuration-1.6.jar
[INFO] Copying httpcore-4.3.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/httpcore-4.3.1.jar
[INFO] Copying hadoop-yarn-api-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-yarn-api-2.5.2.jar
[INFO] Copying jackson-core-asl-1.9.13.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/jackson-core-asl-1.9.13.jar
[INFO] Copying commons-jexl-2.1.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-jexl-2.1.1.jar
[INFO] Copying hadoop-mapreduce-client-jobclient-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-mapreduce-client-jobclient-2.5.2.jar
[INFO] Copying httpclient-4.3.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/httpclient-4.3.2.jar
[INFO] Copying avro-1.7.6.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/avro-1.7.6.jar
[INFO] Copying parquet-column-1.4.3.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/parquet-column-1.4.3.jar
[INFO] Copying bdg-formats-0.2.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/bdg-formats-0.2.0.jar
[INFO] Copying commons-net-3.1.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/commons-net-3.1.jar
[INFO] Copying hadoop-mapreduce-client-shuffle-2.5.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/hadoop-mapreduce-client-shuffle-2.5.2.jar
[INFO] Copying scalac-scoverage-plugin_2.10-0.99.2.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/scalac-scoverage-plugin_2.10-0.99.2.jar
[INFO] Copying asm-4.0.jar to /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/lib/asm-4.0.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ cloud-scale-bwamem ---
[INFO] Including org.scala-lang:scala-library:jar:2.10.3 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-client:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-common:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:11.0.2 in the shaded jar.
[INFO] Including commons-cli:commons-cli:jar:1.2 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.1.1 in the shaded jar.
[INFO] Including xmlenc:xmlenc:jar:0.52 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:3.1 in the shaded jar.
[INFO] Including commons-collections:commons-collections:jar:3.2.1 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including commons-lang:commons-lang:jar:2.6 in the shaded jar.
[INFO] Including commons-configuration:commons-configuration:jar:1.6 in the shaded jar.
[INFO] Including commons-digester:commons-digester:jar:1.8 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils:jar:1.7.0 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils-core:jar:1.8.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:2.5.0 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-auth:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.directory.server:apacheds-kerberos-codec:jar:2.0.0-M15 in the shaded jar.
[INFO] Including org.apache.directory.server:apacheds-i18n:jar:2.0.0-M15 in the shaded jar.
[INFO] Including org.apache.directory.api:api-asn1-api:jar:1.0.0-M20 in the shaded jar.
[INFO] Including org.apache.directory.api:api-util:jar:1.0.0-M20 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-hdfs:jar:2.5.2 in the shaded jar.
[INFO] Including org.mortbay.jetty:jetty-util:jar:6.1.26 in the shaded jar.
[INFO] Including io.netty:netty:jar:3.6.2.Final in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-app:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-common:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-client:jar:2.5.2 in the shaded jar.
[INFO] Including com.sun.jersey:jersey-client:jar:1.9 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-server-common:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-shuffle:jar:2.5.2 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-api:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-core:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-yarn-common:jar:2.5.2 in the shaded jar.
[INFO] Including javax.xml.bind:jaxb-api:jar:2.2.2 in the shaded jar.
[INFO] Including javax.xml.stream:stax-api:jar:1.0-2 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1 in the shaded jar.
[INFO] Including com.sun.jersey:jersey-core:jar:1.9 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-mapreduce-client-jobclient:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-annotations:jar:2.5.2 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.7.6 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.3 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.0 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.6.4 in the shaded jar.
[INFO] Including com.twitter:parquet-avro:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-column:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-common:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-encoding:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-generator:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-hadoop:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-jackson:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-format:jar:2.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.2.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core:jar:0.14.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.21 in the shaded jar.
[INFO] Including com.esotericsoftware.reflectasm:reflectasm:jar:shaded:1.07 in the shaded jar.
[INFO] Including org.ow2.asm:asm:jar:4.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:1.2 in the shaded jar.
[INFO] Including org.scoverage:scalac-scoverage-plugin_2.10:jar:0.99.2 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.4.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.0.0 in the shaded jar.
[INFO] Including org.seqdoop:cofoja:jar:1.1-r150 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.3.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.3.1 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including org.seqdoop:htsjdk:jar:1.118 in the shaded jar.
[INFO] Including org.apache.ant:ant:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.ant:ant-launcher:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.bcel:bcel:jar:5.2 in the shaded jar.
[INFO] Including jakarta-regexp:jakarta-regexp:jar:1.4 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including org.testng:testng:jar:6.8.8 in the shaded jar.
[INFO] Including org.beanshell:bsh:jar:2.0b4 in the shaded jar.
[INFO] Including com.beust:jcommander:jar:1.27 in the shaded jar.
[WARNING] hadoop-yarn-common-2.5.2.jar, hadoop-yarn-api-2.5.2.jar define 3 overlapping classes: 
[WARNING]   - org.apache.hadoop.yarn.factories.package-info
[WARNING]   - org.apache.hadoop.yarn.util.package-info
[WARNING]   - org.apache.hadoop.yarn.factory.providers.package-info
[WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: 
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Tainted
[WARNING]   - javax.annotation.meta.TypeQualifierValidator
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.Nonnull$Checker
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - 24 more...
[WARNING] commons-beanutils-core-1.8.0.jar, commons-beanutils-1.7.0.jar, commons-collections-3.2.1.jar define 10 overlapping classes: 
[WARNING]   - org.apache.commons.collections.FastHashMap$EntrySet
[WARNING]   - org.apache.commons.collections.ArrayStack
[WARNING]   - org.apache.commons.collections.FastHashMap$1
[WARNING]   - org.apache.commons.collections.FastHashMap$KeySet
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView
[WARNING]   - org.apache.commons.collections.BufferUnderflowException
[WARNING]   - org.apache.commons.collections.Buffer
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView$CollectionViewIterator
[WARNING]   - org.apache.commons.collections.FastHashMap$Values
[WARNING]   - org.apache.commons.collections.FastHashMap
[WARNING] minlog-1.2.jar, kryo-2.21.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING] commons-beanutils-core-1.8.0.jar, commons-beanutils-1.7.0.jar define 82 overlapping classes: 
[WARNING]   - org.apache.commons.beanutils.Converter
[WARNING]   - org.apache.commons.beanutils.WrapDynaBean
[WARNING]   - org.apache.commons.beanutils.converters.IntegerConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleBeanUtilsBean
[WARNING]   - org.apache.commons.beanutils.locale.converters.DoubleLocaleConverter
[WARNING]   - org.apache.commons.beanutils.locale.converters.DecimalLocaleConverter
[WARNING]   - org.apache.commons.beanutils.converters.ShortConverter
[WARNING]   - org.apache.commons.beanutils.converters.StringArrayConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleConvertUtilsBean
[WARNING]   - org.apache.commons.beanutils.LazyDynaClass
[WARNING]   - 72 more...
[WARNING] asm-4.0.jar, cofoja-1.1-r150.jar define 22 overlapping classes: 
[WARNING]   - org.objectweb.asm.Item
[WARNING]   - org.objectweb.asm.signature.SignatureWriter
[WARNING]   - org.objectweb.asm.MethodWriter
[WARNING]   - org.objectweb.asm.Type
[WARNING]   - org.objectweb.asm.Opcodes
[WARNING]   - org.objectweb.asm.Handler
[WARNING]   - org.objectweb.asm.MethodVisitor
[WARNING]   - org.objectweb.asm.Label
[WARNING]   - org.objectweb.asm.Handle
[WARNING]   - org.objectweb.asm.FieldWriter
[WARNING]   - 12 more...
[WARNING] kryo-2.21.jar, objenesis-1.2.jar define 32 overlapping classes: 
[WARNING]   - org.objenesis.Objenesis
[WARNING]   - org.objenesis.strategy.StdInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.basic.ObjectStreamClassInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactorySerializationInstantiator
[WARNING]   - org.objenesis.instantiator.perc.PercSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.NullInstantiator
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiatorBase
[WARNING]   - org.objenesis.ObjenesisException
[WARNING]   - org.objenesis.instantiator.basic.ObjectInputStreamInstantiator$MockStream
[WARNING]   - 22 more...
[WARNING] kryo-2.21.jar, reflectasm-1.07-shaded.jar define 23 overlapping classes: 
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Opcodes
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Frame
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Label
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldWriter
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.AnnotationVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Item
[WARNING]   - com.esotericsoftware.reflectasm.AccessClassLoader
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Edge
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ClassVisitor
[WARNING]   - 13 more...
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:21 min
[INFO] Finished at: 2016-06-02T18:54:42+08:00
[INFO] Final Memory: 67M/582M
[INFO] ------------------------------------------------------------------------
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:jniNative:so:0.2.0
[WARNING] 'dependencies.dependency.systemPath' for cs.ucla.edu:cloud-scale-bwamem:jar should use a variable instead of a hard-coded path /home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.0-assembly.jar @ line 19, column 19
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:native-maven-plugin is missing. @ line 33, column 15
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 25, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building JNI Pair-End Smith-Waterman AVX Library 0.2.0
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:initialize (default-initialize) @ jniNative ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:unzipinc (default-unzipinc) @ jniNative ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:javah (default-javah) @ jniNative ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:javah (javah) @ jniNative ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target && javah -o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah/jni_mate_sw.h -classpath /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/classes:/home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.0-assembly.jar cs.ucla.edu.bwaspark.jni.HelloWorld cs.ucla.edu.bwaspark.jni.MateSWType cs.ucla.edu.bwaspark.jni.SeqSWType cs.ucla.edu.bwaspark.jni.MateSWJNI cs.ucla.edu.bwaspark.datatype.MemAlnRegType cs.ucla.edu.bwaspark.datatype.MemOptType cs.ucla.edu.bwaspark.datatype.MemPeStat cs.ucla.edu.bwaspark.datatype.FASTQSingleNode
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:compile (default-compile) @ jniNative ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/jni_hello_world.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/jni_hello_world.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/jni_mate_sw.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/jni_mate_sw.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwt.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/bwt.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwa.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/bwa.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bntseq.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/bntseq.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwamem.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/bwamem.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwamem_pair.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/bwamem_pair.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/ksw.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/ksw.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/kstring.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/kstring.c
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/utils.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/native/utils.c
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:link (default-link) @ jniNative ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src && gcc -shared -lm -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/jniNative.so /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/jni_hello_world.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/jni_mate_sw.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwt.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwa.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bntseq.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwamem.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/bwamem_pair.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/ksw.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/kstring.o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/utils.o
[INFO] 
[INFO] --- maven-resources-plugin:3.0.0:testResources (default-testResources) @ jniNative ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ jniNative ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ jniNative ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:inczip (default-inczip) @ jniNative ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8.451 s
[INFO] Finished at: 2016-06-02T18:54:53+08:00
[INFO] Final Memory: 12M/163M
[INFO] ------------------------------------------------------------------------
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:jniSWExtend:so:0.2.0
[WARNING] 'dependencies.dependency.systemPath' for cs.ucla.edu:cloud-scale-bwamem:jar should use a variable instead of a hard-coded path /home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.0-assembly.jar @ line 19, column 19
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:native-maven-plugin is missing. @ line 33, column 15
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 25, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building JNI Smith-Waterman Extend on FPGA 0.2.0
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:initialize (default-initialize) @ jniSWExtend ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:unzipinc (default-unzipinc) @ jniSWExtend ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:javah (default-javah) @ jniSWExtend ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:javah (javah) @ jniSWExtend ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target && javah -o /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah/jni_sw_extend.h -classpath /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/classes:/home/ytchen/cs-bwamem/0.2.0/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.0-assembly.jar cs.ucla.edu.bwaspark.jni.SWExtendFPGAJNI
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:compile (default-compile) @ jniSWExtend ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/jni_fpga && gcc -s -fPIC -O2 -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/jni_fpga -I/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/custom-javah -I/usr/lib/jvm/jdk1.7.0/jre/../include -I/usr/lib/jvm/jdk1.7.0/jre/../include/linux -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/sw_extend_fpga.o -c /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/jni_fpga/sw_extend_fpga.c
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:link (default-link) @ jniSWExtend ---
[INFO] /bin/sh -c cd /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/jni_fpga && gcc -shared -lrt -o/home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/jniSWExtend.so /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/target/objs/sw_extend_fpga.o
[INFO] 
[INFO] --- maven-resources-plugin:3.0.0:testResources (default-testResources) @ jniSWExtend ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] skip non existing resourceDirectory /home/hadoop/xubo/tools/cloud-scale-bwamem-0.2.1/src/main/jni_fpga/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ jniSWExtend ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ jniSWExtend ---
[INFO] 
[INFO] --- native-maven-plugin:1.0-alpha-8:inczip (default-inczip) @ jniSWExtend ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.478 s
[INFO] Finished at: 2016-06-02T18:54:58+08:00
[INFO] Final Memory: 12M/163M
[INFO] ------------------------------------------------------------------------
hadoop@Master:~/xubo/tools/cloud-scale-bwamem-0.2.1$