Created
August 5, 2015 17:07
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| $ bash -x ./bin/adam-submit --jars adam-plugins_2.10-0.17.1-SNAPSHOT.jar -- plugin com.github.heuermh.adam.plugins.CountAlignments adam-core/src/test/resources/small.sam | |
| + set -e | |
| + DOUBLE_DASH=False | |
| + for ARG in '"$@"' | |
| + [[ --jars == \-\- ]] | |
| + for ARG in '"$@"' | |
| + [[ adam-plugins_2.10-0.17.1-SNAPSHOT.jar == \-\- ]] | |
| + for ARG in '"$@"' | |
| + [[ -- == \-\- ]] | |
| + DOUBLE_DASH=True | |
| + break | |
| + [[ True == \F\a\l\s\e ]] | |
| + SPARK_ARGS=() | |
| + for ARG in '"$@"' | |
| + shift | |
| + [[ --jars == \-\- ]] | |
| + SPARK_ARGS+=("$ARG") | |
| + for ARG in '"$@"' | |
| + shift | |
| + [[ adam-plugins_2.10-0.17.1-SNAPSHOT.jar == \-\- ]] | |
| + SPARK_ARGS+=("$ARG") | |
| + for ARG in '"$@"' | |
| + shift | |
| + [[ -- == \-\- ]] | |
| + ADAM_ARGS='plugin com.github.heuermh.adam.plugins.CountAlignments adam-core/src/test/resources/small.sam' | |
| + break | |
| + SPARK_ARGS='--jars adam-plugins_2.10-0.17.1-SNAPSHOT.jar' | |
| +++ dirname ./bin/adam-submit | |
| ++ cd ./bin/.. | |
| ++ pwd | |
| + SCRIPT_DIR=/Users/mheuer/working/laserson-adam | |
| ++ /Users/mheuer/working/laserson-adam/bin/compute-adam-jars.sh | |
| + ADAM_JARS=/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.1-SNAPSHOT/adam-core_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.1-SNAPSHOT/adam-apis_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar | |
| ++ /Users/mheuer/working/laserson-adam/bin/append_to_option.py , --jars /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.1-SNAPSHOT/adam-core_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.1-SNAPSHOT/adam-apis_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar '--jars adam-plugins_2.10-0.17.1-SNAPSHOT.jar' | |
| + SPARK_ARGS='--jars adam-plugins_2.10-0.17.1-SNAPSHOT.jar --jars /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.1-SNAPSHOT/adam-core_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.1-SNAPSHOT/adam-apis_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar' | |
| + REPO_DIR=/Users/mheuer/working/laserson-adam/repo | |
| + '[' '!' -d /Users/mheuer/working/laserson-adam/repo ']' | |
| + REPO_DIR=/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo | |
| + ADAM_DIR=/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam | |
| ++ ls /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam | |
| ++ grep cli | |
| ++ wc -l | |
| + num_versions=' 1' | |
| + '[' ' 1' -eq 0 ']' | |
| + '[' ' 1' -gt 1 ']' | |
| ++ ls /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam | |
| ++ grep cli | |
| + CLI=adam-cli_2.10 | |
| + CLI_DIR=/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10 | |
| ++ ls /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar | |
| + ADAM_CLI_JAR=/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar | |
| + '[' -z /usr/local/Cellar/apache-spark/1.4.1/libexec ']' | |
| + SPARK_SUBMIT=/usr/local/Cellar/apache-spark/1.4.1/libexec/bin/spark-submit | |
| + /usr/local/Cellar/apache-spark/1.4.1/libexec/bin/spark-submit --class org.bdgenomics.adam.cli.ADAMMain --conf spark.serializer=org.apache.spark.serializer.KryoSerializer --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator --jars adam-plugins_2.10-0.17.1-SNAPSHOT.jar --jars /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.1-SNAPSHOT/adam-core_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.1-SNAPSHOT/adam-apis_2.10-0.17.1-SNAPSHOT.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar,/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar /Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar plugin com.github.heuermh.adam.plugins.CountAlignments adam-core/src/test/resources/small.sam | |
| Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties | |
| 15/08/05 12:06:04 INFO ADAMMain: ADAM invoked with args: "plugin" "com.github.heuermh.adam.plugins.CountAlignments" "adam-core/src/test/resources/small.sam" | |
| 15/08/05 12:06:04 INFO SparkContext: Running Spark version 1.4.1 | |
| 15/08/05 12:06:04 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable | |
| 15/08/05 12:06:05 INFO SecurityManager: Changing view acls to: mheuer | |
| 15/08/05 12:06:05 INFO SecurityManager: Changing modify acls to: mheuer | |
| 15/08/05 12:06:05 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(mheuer); users with modify permissions: Set(mheuer) | |
| 15/08/05 12:06:05 INFO Slf4jLogger: Slf4jLogger started | |
| 15/08/05 12:06:05 INFO Remoting: Starting remoting | |
| 15/08/05 12:06:05 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkDriver@192.168.1.6:49909] | |
| 15/08/05 12:06:05 INFO Utils: Successfully started service 'sparkDriver' on port 49909. | |
| 15/08/05 12:06:05 INFO SparkEnv: Registering MapOutputTracker | |
| 15/08/05 12:06:05 INFO SparkEnv: Registering BlockManagerMaster | |
| 15/08/05 12:06:06 INFO DiskBlockManager: Created local directory at /private/var/folders/8f/5r73k3zs4dq2j968n458d7j80000gn/T/spark-be7a4b50-2bb0-4247-97ae-64eeb2ece933/blockmgr-014b0f44-cdde-493c-8a6b-c34913bdd9ed | |
| 15/08/05 12:06:06 INFO MemoryStore: MemoryStore started with capacity 265.1 MB | |
| 15/08/05 12:06:06 INFO HttpFileServer: HTTP File server directory is /private/var/folders/8f/5r73k3zs4dq2j968n458d7j80000gn/T/spark-be7a4b50-2bb0-4247-97ae-64eeb2ece933/httpd-0bdb151a-861b-4304-8a6c-1ce252b028ff | |
| 15/08/05 12:06:06 INFO HttpServer: Starting HTTP Server | |
| 15/08/05 12:06:06 INFO Utils: Successfully started service 'HTTP file server' on port 49910. | |
| 15/08/05 12:06:06 INFO SparkEnv: Registering OutputCommitCoordinator | |
| 15/08/05 12:06:06 INFO Utils: Successfully started service 'SparkUI' on port 4040. | |
| 15/08/05 12:06:06 INFO SparkUI: Started SparkUI at http://192.168.1.6:4040 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar at http://192.168.1.6:49910/jars/commons-cli-1.2.jar with timestamp 1438794366388 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar at http://192.168.1.6:49910/jars/commons-httpclient-3.1.jar with timestamp 1438794366390 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar at http://192.168.1.6:49910/jars/commons-codec-1.4.jar with timestamp 1438794366391 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar at http://192.168.1.6:49910/jars/commons-logging-1.1.1.jar with timestamp 1438794366392 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar at http://192.168.1.6:49910/jars/commons-compress-1.4.1.jar with timestamp 1438794366393 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar at http://192.168.1.6:49910/jars/slf4j-api-1.7.10.jar with timestamp 1438794366394 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar at http://192.168.1.6:49910/jars/log4j-1.2.17.jar with timestamp 1438794366397 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar at http://192.168.1.6:49910/jars/snappy-java-1.1.1.7.jar with timestamp 1438794366400 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar at http://192.168.1.6:49910/jars/paranamer-2.6.jar with timestamp 1438794366401 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar at http://192.168.1.6:49910/jars/utils-io_2.10-0.2.2.jar with timestamp 1438794366401 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar at http://192.168.1.6:49910/jars/utils-misc_2.10-0.2.2.jar with timestamp 1438794366401 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar at http://192.168.1.6:49910/jars/httpclient-4.3.2.jar with timestamp 1438794366403 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar at http://192.168.1.6:49910/jars/httpcore-4.3.1.jar with timestamp 1438794366404 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar at http://192.168.1.6:49910/jars/utils-cli_2.10-0.2.2.jar with timestamp 1438794366405 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-avro-1.8.1.jar with timestamp 1438794366406 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-column-1.8.1.jar with timestamp 1438794366408 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-common-1.8.1.jar with timestamp 1438794366409 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-encoding-1.8.1.jar with timestamp 1438794366410 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-hadoop-1.8.1.jar with timestamp 1438794366412 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-jackson-1.8.1.jar with timestamp 1438794366417 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar at http://192.168.1.6:49910/jars/parquet-format-2.3.0-incubating.jar with timestamp 1438794366419 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar at http://192.168.1.6:49910/jars/utils-metrics_2.10-0.2.2.jar with timestamp 1438794366422 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar at http://192.168.1.6:49910/jars/servo-core-0.5.5.jar with timestamp 1438794366424 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar at http://192.168.1.6:49910/jars/annotations-2.0.0.jar with timestamp 1438794366426 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar at http://192.168.1.6:49910/jars/scalac-scoverage-plugin_2.10-0.99.2.jar with timestamp 1438794366428 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar at http://192.168.1.6:49910/jars/commons-io-1.3.2.jar with timestamp 1438794366430 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar at http://192.168.1.6:49910/jars/bdg-formats-0.4.0.jar with timestamp 1438794366431 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar at http://192.168.1.6:49910/jars/avro-1.7.6.jar with timestamp 1438794366432 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar at http://192.168.1.6:49910/jars/jackson-core-asl-1.9.13.jar with timestamp 1438794366433 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar at http://192.168.1.6:49910/jars/jackson-mapper-asl-1.9.13.jar with timestamp 1438794366436 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.1-SNAPSHOT/adam-core_2.10-0.17.1-SNAPSHOT.jar at http://192.168.1.6:49910/jars/adam-core_2.10-0.17.1-SNAPSHOT.jar with timestamp 1438794366440 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar at http://192.168.1.6:49910/jars/kryo-2.21.jar with timestamp 1438794366443 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar at http://192.168.1.6:49910/jars/reflectasm-1.07-shaded.jar with timestamp 1438794366443 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar at http://192.168.1.6:49910/jars/asm-4.0.jar with timestamp 1438794366447 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar at http://192.168.1.6:49910/jars/minlog-1.2.jar with timestamp 1438794366447 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar at http://192.168.1.6:49910/jars/objenesis-1.2.jar with timestamp 1438794366448 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar at http://192.168.1.6:49910/jars/fastutil-6.4.4.jar with timestamp 1438794366485 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.1/parquet-scala_2.10-1.8.1.jar at http://192.168.1.6:49910/jars/parquet-scala_2.10-1.8.1.jar with timestamp 1438794366486 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar at http://192.168.1.6:49910/jars/hadoop-bam-7.0.0.jar with timestamp 1438794366487 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar at http://192.168.1.6:49910/jars/htsjdk-1.133.jar with timestamp 1438794366499 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar at http://192.168.1.6:49910/jars/commons-jexl-2.1.1.jar with timestamp 1438794366500 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar at http://192.168.1.6:49910/jars/xz-1.5.jar with timestamp 1438794366501 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar at http://192.168.1.6:49910/jars/ant-1.8.2.jar with timestamp 1438794366504 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar at http://192.168.1.6:49910/jars/ant-launcher-1.8.2.jar with timestamp 1438794366505 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar at http://192.168.1.6:49910/jars/testng-6.8.8.jar with timestamp 1438794366509 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar at http://192.168.1.6:49910/jars/bsh-2.0b4.jar with timestamp 1438794366512 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar at http://192.168.1.6:49910/jars/jcommander-1.27.jar with timestamp 1438794366513 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar at http://192.168.1.6:49910/jars/guava-14.0.1.jar with timestamp 1438794366520 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.1-SNAPSHOT/adam-apis_2.10-0.17.1-SNAPSHOT.jar at http://192.168.1.6:49910/jars/adam-apis_2.10-0.17.1-SNAPSHOT.jar with timestamp 1438794366521 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar at http://192.168.1.6:49910/jars/scala-library-2.10.4.jar with timestamp 1438794366535 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar at http://192.168.1.6:49910/jars/slf4j-log4j12-1.7.5.jar with timestamp 1438794366536 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar at http://192.168.1.6:49910/jars/args4j-2.0.23.jar with timestamp 1438794366537 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar at http://192.168.1.6:49910/jars/adam-cli_2.10-0.17.1-SNAPSHOT.jar with timestamp 1438794366537 | |
| 15/08/05 12:06:06 INFO SparkContext: Added JAR file:/Users/mheuer/working/laserson-adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.1-SNAPSHOT/adam-cli_2.10-0.17.1-SNAPSHOT.jar at http://192.168.1.6:49910/jars/adam-cli_2.10-0.17.1-SNAPSHOT.jar with timestamp 1438794366542 | |
| 15/08/05 12:06:06 INFO Executor: Starting executor ID driver on host localhost | |
| 15/08/05 12:06:06 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 49911. | |
| 15/08/05 12:06:06 INFO NettyBlockTransferService: Server created on 49911 | |
| 15/08/05 12:06:06 INFO BlockManagerMaster: Trying to register BlockManager | |
| 15/08/05 12:06:06 INFO BlockManagerMasterEndpoint: Registering block manager localhost:49911 with 265.1 MB RAM, BlockManagerId(driver, localhost, 49911) | |
| 15/08/05 12:06:06 INFO BlockManagerMaster: Registered BlockManager | |
| Exception in thread "main" java.lang.ClassNotFoundException: com.github.heuermh.adam.plugins.CountAlignments | |
| at java.net.URLClassLoader.findClass(URLClassLoader.java:381) | |
| at java.lang.ClassLoader.loadClass(ClassLoader.java:424) | |
| at java.lang.ClassLoader.loadClass(ClassLoader.java:357) | |
| at org.bdgenomics.adam.cli.PluginExecutor.loadPlugin(PluginExecutor.scala:72) | |
| at org.bdgenomics.adam.cli.PluginExecutor.run(PluginExecutor.scala:90) | |
| at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:53) | |
| at org.bdgenomics.adam.cli.PluginExecutor.run(PluginExecutor.scala:66) | |
| at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:106) | |
| at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala) | |
| at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) | |
| at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) | |
| at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) | |
| at java.lang.reflect.Method.invoke(Method.java:497) | |
| at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:665) | |
| at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:170) | |
| at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:193) | |
| at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:112) | |
| at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) | |
| 15/08/05 12:06:06 INFO SparkContext: Invoking stop() from shutdown hook | |
| 15/08/05 12:06:07 INFO SparkUI: Stopped Spark web UI at http://192.168.1.6:4040 | |
| 15/08/05 12:06:07 INFO DAGScheduler: Stopping DAGScheduler | |
| 15/08/05 12:06:07 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped! | |
| 15/08/05 12:06:07 INFO Utils: path = /private/var/folders/8f/5r73k3zs4dq2j968n458d7j80000gn/T/spark-be7a4b50-2bb0-4247-97ae-64eeb2ece933/blockmgr-014b0f44-cdde-493c-8a6b-c34913bdd9ed, already present as root for deletion. | |
| 15/08/05 12:06:07 INFO MemoryStore: MemoryStore cleared | |
| 15/08/05 12:06:07 INFO BlockManager: BlockManager stopped | |
| 15/08/05 12:06:07 INFO BlockManagerMaster: BlockManagerMaster stopped | |
| 15/08/05 12:06:07 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped! | |
| 15/08/05 12:06:07 INFO SparkContext: Successfully stopped SparkContext | |
| 15/08/05 12:06:07 INFO Utils: Shutdown hook called | |
| 15/08/05 12:06:07 INFO Utils: Deleting directory /private/var/folders/8f/5r73k3zs4dq2j968n458d7j80000gn/T/spark-be7a4b50-2bb0-4247-97ae-64eeb2ece933 |
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