基因数据处理25之avocado安装

基因数据处理25之avocado安装

下载:

git clone https://github.com/bigdatagenomics/avocado.git


安装


第一次失败,第二次成功

hadoop@Master:~/cloud/adam/xubo/code/avocado$ mvn install
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.1.5/scala-maven-plugin-3.1.5.pom
Downloaded: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.1.5/scala-maven-plugin-3.1.5.pom (15 KB at 1.3 KB/sec)
Downloading: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.1.5/scala-maven-plugin-3.1.5.jar
Downloaded: https://repo.maven.apache.org/maven2/net/alchim31/maven/scala-maven-plugin/3.1.5/scala-maven-plugin-3.1.5.jar (103 KB at 38.2 KB/sec)
[INFO] 
。。。。。。
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
model contains 76 documentable templates
/home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/src/main/scala/org/bdgenomics/avocado/algorithms/math/LogPhred.scala:26: warning: no additional content on same line after heading
  /**
  ^
one warning found
[INFO] Building jar: /home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/target/avocado-core-0.0.3-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ avocado-core ---
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/target/avocado-core-0.0.3-SNAPSHOT.jar to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-core/0.0.3-SNAPSHOT/avocado-core-0.0.3-SNAPSHOT.jar
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/pom.xml to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-core/0.0.3-SNAPSHOT/avocado-core-0.0.3-SNAPSHOT.pom
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/target/avocado-core-0.0.3-SNAPSHOT-javadoc.jar to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-core/0.0.3-SNAPSHOT/avocado-core-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/appassembler-maven-plugin/1.8/appassembler-maven-plugin-1.8.pom
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Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli_2.10/0.18.2/adam-cli_2.10-0.18.2.pom
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Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar
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Downloaded: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli_2.10/0.18.2/adam-cli_2.10-0.18.2.jar (41623 KB at 1114.2 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ avocado-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 1 Scala source to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/scala-2.10.3/classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ avocado-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ avocado-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ avocado-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ avocado-cli ---
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 150 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ avocado-cli ---
[INFO] Building jar: /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/avocado-cli-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.8:assemble (default) @ avocado-cli ---
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/appassembler/appassembler-model/1.8/appassembler-model-1.8.pom
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[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/utils/utils-cli_2.10/0.2.3/utils-cli_2.10-0.2.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.3/utils-cli_2.10-0.2.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/utils/utils-misc_2.10/0.2.3/utils-misc_2.10-0.2.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.3/utils-misc_2.10-0.2.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/utils/utils-metrics_2.10/0.2.3/utils-metrics_2.10-0.2.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.3/utils-metrics_2.10-0.2.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/args4j/args4j/2.0.23/args4j-2.0.23.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar
[INFO] Installing artifact /home/hadoop/cloud/adam/xubo/code/avocado/avocado-core/target/avocado-core-0.0.3-SNAPSHOT.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/avocado/avocado-core/0.0.3-SNAPSHOT/avocado-core-0.0.3-SNAPSHOT.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/adam/adam-core_2.10/0.18.2/adam-core_2.10-0.18.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.18.2/adam-core_2.10-0.18.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/utils/utils-io_2.10/0.2.3/utils-io_2.10-0.2.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.3/utils-io_2.10-0.2.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/scoverage/scalac-scoverage-plugin_2.10/1.1.1/scalac-scoverage-plugin_2.10-1.1.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/1.1.1/scalac-scoverage-plugin_2.10-1.1.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.6.1/bdg-formats-0.6.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.6.1/bdg-formats-0.6.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/it/unimi/dsi/fastutil/6.6.5/fastutil-6.6.5.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.6.5/fastutil-6.6.5.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/avro/avro/1.7.7/avro-1.7.7.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/avro/avro/1.7.7/avro-1.7.7.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/seqdoop/hadoop-bam/7.1.0/hadoop-bam-7.1.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.1.0/hadoop-bam-7.1.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/github/samtools/htsjdk/1.139/htsjdk-1.139.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.139/htsjdk-1.139.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/ant/ant/1.8.2/ant-1.8.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/httpcomponents/httpclient/4.5.1/httpclient-4.5.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.1/httpclient-4.5.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/apache/httpcomponents/httpcore/4.4.3/httpcore-4.4.3.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.3/httpcore-4.4.3.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/netflix/servo/servo-core/0.10.0/servo-core-0.10.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.10.0/servo-core-0.10.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/netflix/servo/servo-internal/0.10.0/servo-internal-0.10.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/netflix/servo/servo-internal/0.10.0/servo-internal-0.10.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/google/guava/guava/16.0.1/guava-16.0.1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/google/guava/guava/16.0.1/guava-16.0.1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/adam/adam-cli_2.10/0.18.2/adam-cli_2.10-0.18.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.18.2/adam-cli_2.10-0.18.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/bdgenomics/adam/adam-apis_2.10/0.18.2/adam-apis_2.10-0.18.2.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.18.2/adam-apis_2.10-0.18.2.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/net/codingwell/scala-guice_2.10/4.0.0/scala-guice_2.10-4.0.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/net/codingwell/scala-guice_2.10/4.0.0/scala-guice_2.10-4.0.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/google/inject/guice/4.0/guice-4.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/google/inject/guice/4.0/guice-4.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/google/inject/extensions/guice-multibindings/4.0/guice-multibindings-4.0.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/google/inject/extensions/guice-multibindings/4.0/guice-multibindings-4.0.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar
[INFO] Installing artifact /home/hadoop/.m2/repository/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar
[INFO] Installing artifact /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/avocado-cli-0.0.3-SNAPSHOT.jar to /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/appassembler/repo/org/bdgenomics/avocado/avocado-cli/0.0.3-SNAPSHOT/avocado-cli-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) > generate-sources @ avocado-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) < generate-sources @ avocado-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ avocado-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.3 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
model contains 8 documentable templates
[INFO] Building jar: /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/avocado-cli-0.0.3-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ avocado-cli ---
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/avocado-cli-0.0.3-SNAPSHOT.jar to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-cli/0.0.3-SNAPSHOT/avocado-cli-0.0.3-SNAPSHOT.jar
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/pom.xml to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-cli/0.0.3-SNAPSHOT/avocado-cli-0.0.3-SNAPSHOT.pom
[INFO] Installing /home/hadoop/cloud/adam/xubo/code/avocado/avocado-cli/target/avocado-cli-0.0.3-SNAPSHOT-javadoc.jar to /home/hadoop/.m2/repository/org/bdgenomics/avocado/avocado-cli/0.0.3-SNAPSHOT/avocado-cli-0.0.3-SNAPSHOT-javadoc.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [  5.971 s]
[INFO] avocado-core: Core variant calling algorithms ...... SUCCESS [05:13 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SUCCESS [01:51 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 07:11 min
[INFO] Finished at: 2016-04-23T02:16:39+08:00
[INFO] Final Memory: 34M/534M
[INFO] ------------------------------------------------------------------------

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