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Created August 23, 2015 22:40
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SAM header being un-set
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gistfile1.txt
$ rm -f sorted.sam && bin/adam-submit transform -single -sort_reads adam-cli/src/test/resources/bqsr1.sam sorted.sam
Using SPARK_SUBMIT=/Users/ryan/sparks/spark-1.4.1-bin-hadoop2.4/bin/spark-submit
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
15/08/23 22:33:48 INFO ADAMMain: ADAM invoked with args: "transform" "-single" "-sort_reads" "adam-cli/src/test/resources/bqsr1.sam" "sorted.sam"
15/08/23 22:33:48 INFO SparkContext: Running Spark version 1.4.1
15/08/23 22:33:48 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/08/23 22:33:48 INFO SecurityManager: Changing view acls to: ryan
15/08/23 22:33:48 INFO SecurityManager: Changing modify acls to: ryan
15/08/23 22:33:48 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(ryan); users with modify permissions: Set(ryan)
15/08/23 22:33:49 INFO Slf4jLogger: Slf4jLogger started
15/08/23 22:33:49 INFO Remoting: Starting remoting
15/08/23 22:33:49 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkDriver@192.168.0.8:60424]
15/08/23 22:33:49 INFO Utils: Successfully started service 'sparkDriver' on port 60424.
15/08/23 22:33:49 INFO SparkEnv: Registering MapOutputTracker
15/08/23 22:33:49 INFO SparkEnv: Registering BlockManagerMaster
15/08/23 22:33:49 INFO DiskBlockManager: Created local directory at /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/blockmgr-13d3008f-5fda-4282-ad50-e18b82b5211b
15/08/23 22:33:49 INFO MemoryStore: MemoryStore started with capacity 265.4 MB
15/08/23 22:33:49 INFO HttpFileServer: HTTP File server directory is /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/httpd-b4b618a4-ea86-44fb-80ef-ed23a0d383d3
15/08/23 22:33:49 INFO HttpServer: Starting HTTP Server
15/08/23 22:33:50 INFO Utils: Successfully started service 'HTTP file server' on port 60425.
15/08/23 22:33:50 INFO SparkEnv: Registering OutputCommitCoordinator
15/08/23 22:33:50 INFO Utils: Successfully started service 'SparkUI' on port 4040.
15/08/23 22:33:50 INFO SparkUI: Started SparkUI at http://192.168.0.8:4040
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar at http://192.168.0.8:60425/jars/commons-cli-1.2.jar with timestamp 1440369230321
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar at http://192.168.0.8:60425/jars/commons-httpclient-3.1.jar with timestamp 1440369230324
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar at http://192.168.0.8:60425/jars/commons-codec-1.4.jar with timestamp 1440369230325
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar at http://192.168.0.8:60425/jars/commons-logging-1.1.1.jar with timestamp 1440369230325
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar at http://192.168.0.8:60425/jars/commons-compress-1.4.1.jar with timestamp 1440369230326
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar at http://192.168.0.8:60425/jars/slf4j-api-1.7.10.jar with timestamp 1440369230330
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar at http://192.168.0.8:60425/jars/log4j-1.2.17.jar with timestamp 1440369230332
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.7/snappy-java-1.1.1.7.jar at http://192.168.0.8:60425/jars/snappy-java-1.1.1.7.jar with timestamp 1440369230336
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.6/paranamer-2.6.jar at http://192.168.0.8:60425/jars/paranamer-2.6.jar with timestamp 1440369230336
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/utils-io_2.10-0.2.2.jar with timestamp 1440369230337
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/utils-misc_2.10-0.2.2.jar with timestamp 1440369230337
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar at http://192.168.0.8:60425/jars/httpclient-4.3.2.jar with timestamp 1440369230339
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar at http://192.168.0.8:60425/jars/httpcore-4.3.1.jar with timestamp 1440369230341
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/amazonaws/aws-java-sdk/1.7.5/aws-java-sdk-1.7.5.jar at http://192.168.0.8:60425/jars/aws-java-sdk-1.7.5.jar with timestamp 1440369230410
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/joda-time/joda-time/2.8.2/joda-time-2.8.2.jar at http://192.168.0.8:60425/jars/joda-time-2.8.2.jar with timestamp 1440369230413
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/utils-cli_2.10-0.2.2.jar with timestamp 1440369230415
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-avro-1.8.1.jar with timestamp 1440369230416
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.1/parquet-column-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-column-1.8.1.jar with timestamp 1440369230419
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.1/parquet-common-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-common-1.8.1.jar with timestamp 1440369230419
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.1/parquet-encoding-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-encoding-1.8.1.jar with timestamp 1440369230420
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.8.1/parquet-hadoop-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-hadoop-1.8.1.jar with timestamp 1440369230421
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.8.1/parquet-jackson-1.8.1.jar at http://192.168.0.8:60425/jars/parquet-jackson-1.8.1.jar with timestamp 1440369230423
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar at http://192.168.0.8:60425/jars/parquet-format-2.3.0-incubating.jar with timestamp 1440369230425
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/utils-metrics_2.10-0.2.2.jar with timestamp 1440369230429
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar at http://192.168.0.8:60425/jars/servo-core-0.5.5.jar with timestamp 1440369230430
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar at http://192.168.0.8:60425/jars/annotations-2.0.0.jar with timestamp 1440369230431
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/scalac-scoverage-plugin_2.10-0.99.2.jar with timestamp 1440369230432
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar at http://192.168.0.8:60425/jars/commons-io-1.3.2.jar with timestamp 1440369230433
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar at http://192.168.0.8:60425/jars/bdg-formats-0.4.0.jar with timestamp 1440369230433
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar at http://192.168.0.8:60425/jars/avro-1.7.6.jar with timestamp 1440369230434
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar at http://192.168.0.8:60425/jars/jackson-core-asl-1.9.13.jar with timestamp 1440369230435
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar at http://192.168.0.8:60425/jars/jackson-mapper-asl-1.9.13.jar with timestamp 1440369230437
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.2-SNAPSHOT/adam-core_2.10-0.17.2-SNAPSHOT.jar at http://192.168.0.8:60425/jars/adam-core_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230440
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar at http://192.168.0.8:60425/jars/kryo-2.21.jar with timestamp 1440369230442
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar at http://192.168.0.8:60425/jars/reflectasm-1.07-shaded.jar with timestamp 1440369230443
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar at http://192.168.0.8:60425/jars/asm-4.0.jar with timestamp 1440369230443
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar at http://192.168.0.8:60425/jars/minlog-1.2.jar with timestamp 1440369230444
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar at http://192.168.0.8:60425/jars/objenesis-1.2.jar with timestamp 1440369230444
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar at http://192.168.0.8:60425/jars/fastutil-6.4.4.jar with timestamp 1440369230500
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/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://192.168.0.8:60425/jars/parquet-scala_2.10-1.8.1.jar with timestamp 1440369230501
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar at http://192.168.0.8:60425/jars/hadoop-bam-7.0.0.jar with timestamp 1440369230501
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.133/htsjdk-1.133.jar at http://192.168.0.8:60425/jars/htsjdk-1.133.jar with timestamp 1440369230504
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar at http://192.168.0.8:60425/jars/commons-jexl-2.1.1.jar with timestamp 1440369230505
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar at http://192.168.0.8:60425/jars/xz-1.5.jar with timestamp 1440369230506
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/ant/ant/1.8.2/ant-1.8.2.jar at http://192.168.0.8:60425/jars/ant-1.8.2.jar with timestamp 1440369230513
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/apache/ant/ant-launcher/1.8.2/ant-launcher-1.8.2.jar at http://192.168.0.8:60425/jars/ant-launcher-1.8.2.jar with timestamp 1440369230513
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/testng/testng/6.8.8/testng-6.8.8.jar at http://192.168.0.8:60425/jars/testng-6.8.8.jar with timestamp 1440369230516
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar at http://192.168.0.8:60425/jars/bsh-2.0b4.jar with timestamp 1440369230518
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/beust/jcommander/1.27/jcommander-1.27.jar at http://192.168.0.8:60425/jars/jcommander-1.27.jar with timestamp 1440369230518
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar at http://192.168.0.8:60425/jars/guava-14.0.1.jar with timestamp 1440369230524
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis_2.10/0.17.2-SNAPSHOT/adam-apis_2.10-0.17.2-SNAPSHOT.jar at http://192.168.0.8:60425/jars/adam-apis_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230525
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar at http://192.168.0.8:60425/jars/scala-library-2.10.4.jar with timestamp 1440369230556
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar at http://192.168.0.8:60425/jars/slf4j-log4j12-1.7.5.jar with timestamp 1440369230557
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar at http://192.168.0.8:60425/jars/args4j-2.0.23.jar with timestamp 1440369230557
15/08/23 22:33:50 INFO SparkContext: Added JAR file:/Users/ryan/c/adam/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli_2.10/0.17.2-SNAPSHOT/adam-cli_2.10-0.17.2-SNAPSHOT.jar at http://192.168.0.8:60425/jars/adam-cli_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230560
15/08/23 22:33:50 INFO Executor: Starting executor ID driver on host localhost
15/08/23 22:33:50 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 60426.
15/08/23 22:33:50 INFO NettyBlockTransferService: Server created on 60426
15/08/23 22:33:50 INFO BlockManagerMaster: Trying to register BlockManager
15/08/23 22:33:50 INFO BlockManagerMasterEndpoint: Registering block manager localhost:60426 with 265.4 MB RAM, BlockManagerId(driver, localhost, 60426)
15/08/23 22:33:50 INFO BlockManagerMaster: Registered BlockManager
15/08/23 22:33:51 INFO ADAMContext: Loading adam-cli/src/test/resources/bqsr1.sam as SAM/BAM and converting to AlignmentRecords. Projection is ignored.
15/08/23 22:33:51 INFO ADAMContext: Loaded header from file:/Users/ryan/c/adam/adam-cli/src/test/resources/bqsr1.sam
15/08/23 22:33:51 INFO MemoryStore: ensureFreeSpace(183064) called with curMem=0, maxMem=278302556
15/08/23 22:33:51 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 178.8 KB, free 265.2 MB)
15/08/23 22:33:52 INFO MemoryStore: ensureFreeSpace(17309) called with curMem=183064, maxMem=278302556
15/08/23 22:33:52 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 16.9 KB, free 265.2 MB)
15/08/23 22:33:52 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on localhost:60426 (size: 16.9 KB, free: 265.4 MB)
15/08/23 22:33:52 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:263
15/08/23 22:33:52 INFO Transform: Sorting reads
15/08/23 22:33:52 INFO AlignmentRecordRDDFunctions: Sorting reads by reference position
15/08/23 22:33:52 INFO FileInputFormat: Total input paths to process : 1
15/08/23 22:33:52 INFO AlignmentRecordRDDFunctions: Saving data in SAM format
adamSAMSave: true
15/08/23 22:33:52 INFO SparkContext: Starting job: reduce at ADAMRDDFunctions.scala:122
15/08/23 22:33:52 INFO DAGScheduler: Registering RDD 2 (keyBy at AlignmentRecordRDDFunctions.scala:295)
15/08/23 22:33:52 INFO DAGScheduler: Got job 0 (reduce at ADAMRDDFunctions.scala:122) with 1 output partitions (allowLocal=false)
15/08/23 22:33:52 INFO DAGScheduler: Final stage: ResultStage 1(reduce at ADAMRDDFunctions.scala:122)
15/08/23 22:33:52 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
15/08/23 22:33:52 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
15/08/23 22:33:52 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at keyBy at AlignmentRecordRDDFunctions.scala:295), which has no missing parents
15/08/23 22:33:52 INFO MemoryStore: ensureFreeSpace(11120) called with curMem=200373, maxMem=278302556
15/08/23 22:33:52 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 10.9 KB, free 265.2 MB)
15/08/23 22:33:52 INFO MemoryStore: ensureFreeSpace(5377) called with curMem=211493, maxMem=278302556
15/08/23 22:33:52 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 5.3 KB, free 265.2 MB)
15/08/23 22:33:52 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on localhost:60426 (size: 5.3 KB, free: 265.4 MB)
15/08/23 22:33:52 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:52 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at keyBy at AlignmentRecordRDDFunctions.scala:295)
15/08/23 22:33:52 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
15/08/23 22:33:52 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, PROCESS_LOCAL, 4857 bytes)
15/08/23 22:33:52 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/jackson-core-asl-1.9.13.jar with timestamp 1440369230435
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/jackson-core-asl-1.9.13.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp9149802110208090948.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/jackson-core-asl-1.9.13.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/utils-metrics_2.10-0.2.2.jar with timestamp 1440369230429
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/utils-metrics_2.10-0.2.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1806648952788731389.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/utils-metrics_2.10-0.2.2.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-codec-1.4.jar with timestamp 1440369230325
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-codec-1.4.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp7435674868488748430.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-codec-1.4.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/scala-library-2.10.4.jar with timestamp 1440369230556
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/scala-library-2.10.4.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp7066858947207324295.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/scala-library-2.10.4.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-httpclient-3.1.jar with timestamp 1440369230324
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-httpclient-3.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp9043817321033741743.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-httpclient-3.1.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/bdg-formats-0.4.0.jar with timestamp 1440369230433
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/bdg-formats-0.4.0.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp216882903218360916.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/bdg-formats-0.4.0.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/jackson-mapper-asl-1.9.13.jar with timestamp 1440369230437
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/jackson-mapper-asl-1.9.13.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5909232433066581258.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/jackson-mapper-asl-1.9.13.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/kryo-2.21.jar with timestamp 1440369230442
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/kryo-2.21.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1258402835754561835.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/kryo-2.21.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-jackson-1.8.1.jar with timestamp 1440369230423
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-jackson-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6687932686093127679.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-jackson-1.8.1.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-jexl-2.1.1.jar with timestamp 1440369230505
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-jexl-2.1.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp461788219673724356.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-jexl-2.1.1.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/hadoop-bam-7.0.0.jar with timestamp 1440369230501
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/hadoop-bam-7.0.0.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4583792661156907208.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/hadoop-bam-7.0.0.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/servo-core-0.5.5.jar with timestamp 1440369230430
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/servo-core-0.5.5.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1857402737558208459.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/servo-core-0.5.5.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/annotations-2.0.0.jar with timestamp 1440369230431
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/annotations-2.0.0.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1074305319696151752.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/annotations-2.0.0.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-io-1.3.2.jar with timestamp 1440369230433
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-io-1.3.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp7072286833004609588.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-io-1.3.2.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/bsh-2.0b4.jar with timestamp 1440369230518
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/bsh-2.0b4.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4364619156960016654.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/bsh-2.0b4.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/paranamer-2.6.jar with timestamp 1440369230336
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/paranamer-2.6.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5341401975755150042.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/paranamer-2.6.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/snappy-java-1.1.1.7.jar with timestamp 1440369230336
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/snappy-java-1.1.1.7.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6481590361895836363.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/snappy-java-1.1.1.7.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-compress-1.4.1.jar with timestamp 1440369230326
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-compress-1.4.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5450246616922478697.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-compress-1.4.1.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/utils-cli_2.10-0.2.2.jar with timestamp 1440369230415
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/utils-cli_2.10-0.2.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp8776734644850781429.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/utils-cli_2.10-0.2.2.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/log4j-1.2.17.jar with timestamp 1440369230332
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/log4j-1.2.17.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5320466713798886436.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/log4j-1.2.17.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-avro-1.8.1.jar with timestamp 1440369230416
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-avro-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4189426142273040938.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-avro-1.8.1.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/utils-io_2.10-0.2.2.jar with timestamp 1440369230337
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/utils-io_2.10-0.2.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp117468486325542882.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/utils-io_2.10-0.2.2.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/adam-apis_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230525
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/adam-apis_2.10-0.17.2-SNAPSHOT.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6249139350741815494.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/adam-apis_2.10-0.17.2-SNAPSHOT.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/xz-1.5.jar with timestamp 1440369230506
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/xz-1.5.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6607614980359524890.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/xz-1.5.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/htsjdk-1.133.jar with timestamp 1440369230504
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/htsjdk-1.133.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp8776797847396691509.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/htsjdk-1.133.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/adam-cli_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230560
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/adam-cli_2.10-0.17.2-SNAPSHOT.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp2814673125429616646.tmp
15/08/23 22:33:52 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/adam-cli_2.10-0.17.2-SNAPSHOT.jar to class loader
15/08/23 22:33:52 INFO Executor: Fetching http://192.168.0.8:60425/jars/fastutil-6.4.4.jar with timestamp 1440369230500
15/08/23 22:33:52 INFO Utils: Fetching http://192.168.0.8:60425/jars/fastutil-6.4.4.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6540012749894801379.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fastutil-6.4.4.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/avro-1.7.6.jar with timestamp 1440369230434
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/avro-1.7.6.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4938623740329485273.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/avro-1.7.6.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-cli-1.2.jar with timestamp 1440369230321
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-cli-1.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp8365244548981301028.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-cli-1.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/jcommander-1.27.jar with timestamp 1440369230518
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/jcommander-1.27.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp8070279175598426730.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/jcommander-1.27.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-scala_2.10-1.8.1.jar with timestamp 1440369230501
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-scala_2.10-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1651549098308617023.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-scala_2.10-1.8.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/slf4j-log4j12-1.7.5.jar with timestamp 1440369230557
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/slf4j-log4j12-1.7.5.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6379809266481810350.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/slf4j-log4j12-1.7.5.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/testng-6.8.8.jar with timestamp 1440369230516
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/testng-6.8.8.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4379113703163122293.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/testng-6.8.8.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/utils-misc_2.10-0.2.2.jar with timestamp 1440369230337
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/utils-misc_2.10-0.2.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4149809846739341386.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/utils-misc_2.10-0.2.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/ant-1.8.2.jar with timestamp 1440369230513
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/ant-1.8.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5102962496247220726.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/ant-1.8.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/asm-4.0.jar with timestamp 1440369230443
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/asm-4.0.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp778199797513805883.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/asm-4.0.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/guava-14.0.1.jar with timestamp 1440369230524
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/guava-14.0.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6817239540259001507.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/guava-14.0.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-format-2.3.0-incubating.jar with timestamp 1440369230425
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-format-2.3.0-incubating.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5459717254844500386.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-format-2.3.0-incubating.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/adam-core_2.10-0.17.2-SNAPSHOT.jar with timestamp 1440369230440
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/adam-core_2.10-0.17.2-SNAPSHOT.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4273209039465826953.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/adam-core_2.10-0.17.2-SNAPSHOT.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/objenesis-1.2.jar with timestamp 1440369230444
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/objenesis-1.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4367410590832943053.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/objenesis-1.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/aws-java-sdk-1.7.5.jar with timestamp 1440369230410
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/aws-java-sdk-1.7.5.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1799782912554794488.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/aws-java-sdk-1.7.5.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/commons-logging-1.1.1.jar with timestamp 1440369230325
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/commons-logging-1.1.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5056402578926362569.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/commons-logging-1.1.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-encoding-1.8.1.jar with timestamp 1440369230420
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-encoding-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp816319990228370287.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-encoding-1.8.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/slf4j-api-1.7.10.jar with timestamp 1440369230330
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/slf4j-api-1.7.10.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp2911439968992731117.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/slf4j-api-1.7.10.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/joda-time-2.8.2.jar with timestamp 1440369230413
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/joda-time-2.8.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp3775736005063462174.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/joda-time-2.8.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-column-1.8.1.jar with timestamp 1440369230419
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-column-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4804961803393809245.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-column-1.8.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/httpclient-4.3.2.jar with timestamp 1440369230339
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/httpclient-4.3.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp7416903883827744499.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/httpclient-4.3.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/scalac-scoverage-plugin_2.10-0.99.2.jar with timestamp 1440369230432
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/scalac-scoverage-plugin_2.10-0.99.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp1625991935401480682.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/scalac-scoverage-plugin_2.10-0.99.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-common-1.8.1.jar with timestamp 1440369230419
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-common-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp6066485652228807752.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-common-1.8.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/args4j-2.0.23.jar with timestamp 1440369230557
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/args4j-2.0.23.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4609644806828116372.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/args4j-2.0.23.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/reflectasm-1.07-shaded.jar with timestamp 1440369230443
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/reflectasm-1.07-shaded.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4754537226864918970.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/reflectasm-1.07-shaded.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/httpcore-4.3.1.jar with timestamp 1440369230341
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/httpcore-4.3.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp2562457756427684688.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/httpcore-4.3.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/ant-launcher-1.8.2.jar with timestamp 1440369230513
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/ant-launcher-1.8.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp8125101525729282724.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/ant-launcher-1.8.2.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/parquet-hadoop-1.8.1.jar with timestamp 1440369230421
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/parquet-hadoop-1.8.1.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp5074517957107191619.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/parquet-hadoop-1.8.1.jar to class loader
15/08/23 22:33:53 INFO Executor: Fetching http://192.168.0.8:60425/jars/minlog-1.2.jar with timestamp 1440369230444
15/08/23 22:33:53 INFO Utils: Fetching http://192.168.0.8:60425/jars/minlog-1.2.jar to /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/fetchFileTemp4119446652653322368.tmp
15/08/23 22:33:53 INFO Executor: Adding file:/private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/userFiles-2d8acc86-7de3-404b-934a-8a4a5db9651a/minlog-1.2.jar to class loader
15/08/23 22:33:53 INFO NewHadoopRDD: Input split: file:/Users/ryan/c/adam/adam-cli/src/test/resources/bqsr1.sam:0+381096
15/08/23 22:33:54 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1930 bytes result sent to driver
15/08/23 22:33:54 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 2432 ms on localhost (1/1)
15/08/23 22:33:54 INFO DAGScheduler: ShuffleMapStage 0 (keyBy at AlignmentRecordRDDFunctions.scala:295) finished in 2.442 s
15/08/23 22:33:54 INFO DAGScheduler: looking for newly runnable stages
15/08/23 22:33:54 INFO DAGScheduler: running: Set()
15/08/23 22:33:54 INFO DAGScheduler: waiting: Set(ResultStage 1)
15/08/23 22:33:54 INFO DAGScheduler: failed: Set()
15/08/23 22:33:54 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool
15/08/23 22:33:54 INFO DAGScheduler: Missing parents for ResultStage 1: List()
15/08/23 22:33:54 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at mapPartitions at ADAMRDDFunctions.scala:121), which is now runnable
15/08/23 22:33:54 INFO MemoryStore: ensureFreeSpace(3904) called with curMem=216870, maxMem=278302556
15/08/23 22:33:54 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 3.8 KB, free 265.2 MB)
15/08/23 22:33:54 INFO MemoryStore: ensureFreeSpace(2050) called with curMem=220774, maxMem=278302556
15/08/23 22:33:54 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 2.0 KB, free 265.2 MB)
15/08/23 22:33:54 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on localhost:60426 (size: 2.0 KB, free: 265.4 MB)
15/08/23 22:33:54 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:54 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at mapPartitions at ADAMRDDFunctions.scala:121)
15/08/23 22:33:54 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
15/08/23 22:33:54 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, PROCESS_LOCAL, 4567 bytes)
15/08/23 22:33:54 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
15/08/23 22:33:54 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
15/08/23 22:33:54 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 8 ms
15/08/23 22:33:55 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1110 bytes result sent to driver
15/08/23 22:33:55 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 512 ms on localhost (1/1)
15/08/23 22:33:55 INFO DAGScheduler: ResultStage 1 (reduce at ADAMRDDFunctions.scala:122) finished in 0.513 s
15/08/23 22:33:55 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool
15/08/23 22:33:55 INFO DAGScheduler: Job 0 finished: reduce at ADAMRDDFunctions.scala:122, took 3.081799 s
15/08/23 22:33:55 INFO SparkContext: Starting job: collect at AlignmentRecordRDDFunctions.scala:230
15/08/23 22:33:55 INFO MapOutputTrackerMaster: Size of output statuses for shuffle 0 is 143 bytes
15/08/23 22:33:55 INFO DAGScheduler: Registering RDD 7 (distinct at AlignmentRecordRDDFunctions.scala:229)
15/08/23 22:33:55 INFO DAGScheduler: Got job 1 (collect at AlignmentRecordRDDFunctions.scala:230) with 1 output partitions (allowLocal=false)
15/08/23 22:33:55 INFO DAGScheduler: Final stage: ResultStage 4(collect at AlignmentRecordRDDFunctions.scala:230)
15/08/23 22:33:55 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 3)
15/08/23 22:33:55 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 3)
15/08/23 22:33:55 INFO DAGScheduler: Submitting ShuffleMapStage 3 (MapPartitionsRDD[7] at distinct at AlignmentRecordRDDFunctions.scala:229), which has no missing parents
15/08/23 22:33:55 INFO MemoryStore: ensureFreeSpace(3936) called with curMem=222824, maxMem=278302556
15/08/23 22:33:55 INFO MemoryStore: Block broadcast_3 stored as values in memory (estimated size 3.8 KB, free 265.2 MB)
15/08/23 22:33:55 INFO MemoryStore: ensureFreeSpace(2167) called with curMem=226760, maxMem=278302556
15/08/23 22:33:55 INFO MemoryStore: Block broadcast_3_piece0 stored as bytes in memory (estimated size 2.1 KB, free 265.2 MB)
15/08/23 22:33:55 INFO BlockManagerInfo: Added broadcast_3_piece0 in memory on localhost:60426 (size: 2.1 KB, free: 265.4 MB)
15/08/23 22:33:55 INFO SparkContext: Created broadcast 3 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:55 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 3 (MapPartitionsRDD[7] at distinct at AlignmentRecordRDDFunctions.scala:229)
15/08/23 22:33:55 INFO TaskSchedulerImpl: Adding task set 3.0 with 1 tasks
15/08/23 22:33:55 INFO TaskSetManager: Starting task 0.0 in stage 3.0 (TID 2, localhost, PROCESS_LOCAL, 4556 bytes)
15/08/23 22:33:55 INFO Executor: Running task 0.0 in stage 3.0 (TID 2)
15/08/23 22:33:55 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
15/08/23 22:33:55 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 13 ms
15/08/23 22:33:55 INFO BlockManagerInfo: Removed broadcast_2_piece0 on localhost:60426 in memory (size: 2.0 KB, free: 265.4 MB)
15/08/23 22:33:55 INFO BlockManagerInfo: Removed broadcast_1_piece0 on localhost:60426 in memory (size: 5.3 KB, free: 265.4 MB)
15/08/23 22:33:55 INFO Executor: Finished task 0.0 in stage 3.0 (TID 2). 1024 bytes result sent to driver
15/08/23 22:33:55 INFO TaskSetManager: Finished task 0.0 in stage 3.0 (TID 2) in 449 ms on localhost (1/1)
15/08/23 22:33:55 INFO DAGScheduler: ShuffleMapStage 3 (distinct at AlignmentRecordRDDFunctions.scala:229) finished in 0.450 s
15/08/23 22:33:55 INFO DAGScheduler: looking for newly runnable stages
15/08/23 22:33:55 INFO DAGScheduler: running: Set()
15/08/23 22:33:55 INFO DAGScheduler: waiting: Set(ResultStage 4)
15/08/23 22:33:55 INFO DAGScheduler: failed: Set()
15/08/23 22:33:55 INFO TaskSchedulerImpl: Removed TaskSet 3.0, whose tasks have all completed, from pool
15/08/23 22:33:55 INFO DAGScheduler: Missing parents for ResultStage 4: List()
15/08/23 22:33:55 INFO DAGScheduler: Submitting ResultStage 4 (MapPartitionsRDD[9] at distinct at AlignmentRecordRDDFunctions.scala:229), which is now runnable
15/08/23 22:33:55 INFO MemoryStore: ensureFreeSpace(3024) called with curMem=206476, maxMem=278302556
15/08/23 22:33:55 INFO MemoryStore: Block broadcast_4 stored as values in memory (estimated size 3.0 KB, free 265.2 MB)
15/08/23 22:33:55 INFO MemoryStore: ensureFreeSpace(1763) called with curMem=209500, maxMem=278302556
15/08/23 22:33:55 INFO MemoryStore: Block broadcast_4_piece0 stored as bytes in memory (estimated size 1763.0 B, free 265.2 MB)
15/08/23 22:33:55 INFO BlockManagerInfo: Added broadcast_4_piece0 in memory on localhost:60426 (size: 1763.0 B, free: 265.4 MB)
15/08/23 22:33:55 INFO SparkContext: Created broadcast 4 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:55 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 4 (MapPartitionsRDD[9] at distinct at AlignmentRecordRDDFunctions.scala:229)
15/08/23 22:33:55 INFO TaskSchedulerImpl: Adding task set 4.0 with 1 tasks
15/08/23 22:33:55 INFO TaskSetManager: Starting task 0.0 in stage 4.0 (TID 3, localhost, PROCESS_LOCAL, 4567 bytes)
15/08/23 22:33:55 INFO Executor: Running task 0.0 in stage 4.0 (TID 3)
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 7 ms
15/08/23 22:33:56 INFO Executor: Finished task 0.0 in stage 4.0 (TID 3). 1022 bytes result sent to driver
15/08/23 22:33:56 INFO TaskSetManager: Finished task 0.0 in stage 4.0 (TID 3) in 53 ms on localhost (1/1)
15/08/23 22:33:56 INFO DAGScheduler: ResultStage 4 (collect at AlignmentRecordRDDFunctions.scala:230) finished in 0.054 s
15/08/23 22:33:56 INFO TaskSchedulerImpl: Removed TaskSet 4.0, whose tasks have all completed, from pool
15/08/23 22:33:56 INFO DAGScheduler: Job 1 finished: collect at AlignmentRecordRDDFunctions.scala:230, took 0.557299 s
setting sort header
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(1696) called with curMem=211263, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_5 stored as values in memory (estimated size 1696.0 B, free 265.2 MB)
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(412) called with curMem=212959, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_5_piece0 stored as bytes in memory (estimated size 412.0 B, free 265.2 MB)
15/08/23 22:33:56 INFO BlockManagerInfo: Added broadcast_5_piece0 in memory on localhost:60426 (size: 412.0 B, free: 265.4 MB)
15/08/23 22:33:56 INFO SparkContext: Created broadcast 5 from broadcast at AlignmentRecordRDDFunctions.scala:258
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(4344) called with curMem=213371, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_6 stored as values in memory (estimated size 4.2 KB, free 265.2 MB)
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(448) called with curMem=217715, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_6_piece0 stored as bytes in memory (estimated size 448.0 B, free 265.2 MB)
15/08/23 22:33:56 INFO BlockManagerInfo: Added broadcast_6_piece0 in memory on localhost:60426 (size: 448.0 B, free: 265.4 MB)
15/08/23 22:33:56 INFO SparkContext: Created broadcast 6 from broadcast at AlignmentRecordRDDFunctions.scala:141
15/08/23 22:33:56 INFO SparkContext: Starting job: count at AlignmentRecordRDDFunctions.scala:163
15/08/23 22:33:56 INFO MapOutputTrackerMaster: Size of output statuses for shuffle 0 is 143 bytes
15/08/23 22:33:56 INFO DAGScheduler: Got job 2 (count at AlignmentRecordRDDFunctions.scala:163) with 1 output partitions (allowLocal=false)
15/08/23 22:33:56 INFO DAGScheduler: Final stage: ResultStage 6(count at AlignmentRecordRDDFunctions.scala:163)
15/08/23 22:33:56 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 5)
15/08/23 22:33:56 INFO DAGScheduler: Missing parents: List()
15/08/23 22:33:56 INFO DAGScheduler: Submitting ResultStage 6 (MapPartitionsRDD[13] at mapPartitionsWithIndex at AlignmentRecordRDDFunctions.scala:142), which has no missing parents
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(4872) called with curMem=218163, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_7 stored as values in memory (estimated size 4.8 KB, free 265.2 MB)
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(2636) called with curMem=223035, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_7_piece0 stored as bytes in memory (estimated size 2.6 KB, free 265.2 MB)
15/08/23 22:33:56 INFO BlockManagerInfo: Added broadcast_7_piece0 in memory on localhost:60426 (size: 2.6 KB, free: 265.4 MB)
15/08/23 22:33:56 INFO SparkContext: Created broadcast 7 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:56 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 6 (MapPartitionsRDD[13] at mapPartitionsWithIndex at AlignmentRecordRDDFunctions.scala:142)
15/08/23 22:33:56 INFO TaskSchedulerImpl: Adding task set 6.0 with 1 tasks
15/08/23 22:33:56 INFO TaskSetManager: Starting task 0.0 in stage 6.0 (TID 4, localhost, PROCESS_LOCAL, 4567 bytes)
15/08/23 22:33:56 INFO Executor: Running task 0.0 in stage 6.0 (TID 4)
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 6 ms
15/08/23 22:33:56 INFO AlignmentRecordRDDFunctions: Setting SAM header for partition 0
Init ADAMSAMOutputFormat: org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9
clear header: None
add header: SAMFileHeader{VN=1.4, SO=coordinate}
Set SAM header for partition 0: SAMFileHeader{VN=1.4, SO=coordinate}
15/08/23 22:33:56 INFO Executor: Finished task 0.0 in stage 6.0 (TID 4). 844 bytes result sent to driver
15/08/23 22:33:56 INFO TaskSetManager: Finished task 0.0 in stage 6.0 (TID 4) in 279 ms on localhost (1/1)
15/08/23 22:33:56 INFO TaskSchedulerImpl: Removed TaskSet 6.0, whose tasks have all completed, from pool
15/08/23 22:33:56 INFO DAGScheduler: ResultStage 6 (count at AlignmentRecordRDDFunctions.scala:163) finished in 0.281 s
15/08/23 22:33:56 INFO DAGScheduler: Job 2 finished: count at AlignmentRecordRDDFunctions.scala:163, took 0.317187 s
clear header: Some(SAMFileHeader{VN=1.4, SO=coordinate})
add header: SAMFileHeader{VN=1.4, SO=coordinate}
Set SAM header on driver
set header: coordinate coordinate SAMFileHeader{VN=1.4, SO=coordinate}
org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9 return header: Some(SAMFileHeader{VN=1.4, SO=coordinate})
before: SAMFileHeader{VN=1.4, SO=coordinate}
15/08/23 22:33:56 INFO deprecation: mapred.output.dir is deprecated. Instead, use mapreduce.output.fileoutputformat.outputdir
org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9 return header: Some(SAMFileHeader{VN=1.4, SO=coordinate})
got header: SAMFileHeader{VN=1.4, SO=coordinate} from org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9
15/08/23 22:33:56 INFO SparkContext: Starting job: saveAsNewAPIHadoopFile at AlignmentRecordRDDFunctions.scala:188
15/08/23 22:33:56 INFO DAGScheduler: Got job 3 (saveAsNewAPIHadoopFile at AlignmentRecordRDDFunctions.scala:188) with 1 output partitions (allowLocal=false)
15/08/23 22:33:56 INFO DAGScheduler: Final stage: ResultStage 8(saveAsNewAPIHadoopFile at AlignmentRecordRDDFunctions.scala:188)
15/08/23 22:33:56 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 7)
15/08/23 22:33:56 INFO DAGScheduler: Missing parents: List()
15/08/23 22:33:56 INFO DAGScheduler: Submitting ResultStage 8 (CoalescedRDD[12] at coalesce at AlignmentRecordRDDFunctions.scala:138), which has no missing parents
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(59488) called with curMem=225671, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_8 stored as values in memory (estimated size 58.1 KB, free 265.1 MB)
15/08/23 22:33:56 INFO MemoryStore: ensureFreeSpace(20405) called with curMem=285159, maxMem=278302556
15/08/23 22:33:56 INFO MemoryStore: Block broadcast_8_piece0 stored as bytes in memory (estimated size 19.9 KB, free 265.1 MB)
15/08/23 22:33:56 INFO BlockManagerInfo: Added broadcast_8_piece0 in memory on localhost:60426 (size: 19.9 KB, free: 265.4 MB)
15/08/23 22:33:56 INFO SparkContext: Created broadcast 8 from broadcast at DAGScheduler.scala:874
15/08/23 22:33:56 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 8 (CoalescedRDD[12] at coalesce at AlignmentRecordRDDFunctions.scala:138)
15/08/23 22:33:56 INFO TaskSchedulerImpl: Adding task set 8.0 with 1 tasks
15/08/23 22:33:56 INFO TaskSetManager: Starting task 0.0 in stage 8.0 (TID 5, localhost, PROCESS_LOCAL, 4856 bytes)
15/08/23 22:33:56 INFO Executor: Running task 0.0 in stage 8.0 (TID 5)
org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9 return header: Some(SAMFileHeader{VN=1.4, SO=coordinate})
got header: SAMFileHeader{VN=1.4, SO=coordinate} from org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
15/08/23 22:33:56 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 4 ms
15/08/23 22:33:57 INFO BlockManagerInfo: Removed broadcast_7_piece0 on localhost:60426 in memory (size: 2.6 KB, free: 265.4 MB)
15/08/23 22:33:57 INFO BlockManagerInfo: Removed broadcast_4_piece0 on localhost:60426 in memory (size: 1763.0 B, free: 265.4 MB)
15/08/23 22:33:57 INFO BlockManagerInfo: Removed broadcast_3_piece0 on localhost:60426 in memory (size: 2.1 KB, free: 265.4 MB)
15/08/23 22:33:57 INFO ContextCleaner: Cleaned shuffle 1
15/08/23 22:33:57 INFO FileOutputCommitter: Saved output of task 'attempt_201508232233_0012_r_000000_0' to file:/Users/ryan/c/adam/sorted.sam/_temporary/0/task_201508232233_0012_r_000000
15/08/23 22:33:57 INFO Executor: Finished task 0.0 in stage 8.0 (TID 5). 844 bytes result sent to driver
15/08/23 22:33:57 INFO TaskSetManager: Finished task 0.0 in stage 8.0 (TID 5) in 605 ms on localhost (1/1)
15/08/23 22:33:57 INFO DAGScheduler: ResultStage 8 (saveAsNewAPIHadoopFile at AlignmentRecordRDDFunctions.scala:188) finished in 0.605 s
15/08/23 22:33:57 INFO TaskSchedulerImpl: Removed TaskSet 8.0, whose tasks have all completed, from pool
15/08/23 22:33:57 INFO DAGScheduler: Job 3 finished: saveAsNewAPIHadoopFile at AlignmentRecordRDDFunctions.scala:188, took 0.668444 s
org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9 return header: Some(SAMFileHeader{VN=1.4, SO=unsorted})
middle: SAMFileHeader{VN=1.4, SO=unsorted}
Writing single SAM file (not Hadoop-style directory)
org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat$@274bcf9 return header: Some(SAMFileHeader{VN=1.4, SO=unsorted})
after: SAMFileHeader{VN=1.4, SO=unsorted}
15/08/23 22:33:57 INFO Transform: Overall Duration: 8.76 secs
15/08/23 22:33:57 INFO SparkContext: Invoking stop() from shutdown hook
15/08/23 22:33:57 INFO SparkUI: Stopped Spark web UI at http://192.168.0.8:4040
15/08/23 22:33:57 INFO DAGScheduler: Stopping DAGScheduler
15/08/23 22:33:57 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
15/08/23 22:33:57 INFO Utils: path = /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748/blockmgr-13d3008f-5fda-4282-ad50-e18b82b5211b, already present as root for deletion.
15/08/23 22:33:57 INFO MemoryStore: MemoryStore cleared
15/08/23 22:33:57 INFO BlockManager: BlockManager stopped
15/08/23 22:33:57 INFO BlockManagerMaster: BlockManagerMaster stopped
15/08/23 22:33:57 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
15/08/23 22:33:57 INFO SparkContext: Successfully stopped SparkContext
15/08/23 22:33:57 INFO Utils: Shutdown hook called
15/08/23 22:33:57 INFO Utils: Deleting directory /private/var/folders/m0/mj2x82p1527349z6mn8btgtr0000gn/T/spark-099cfe68-025f-45af-9838-7af90e518748
$ head sorted.sam
@HD VN:1.4 SO:unsorted
@SQ SN:14 LN:107349540 M5:14
@SQ SN:22 LN:51304566 M5:22
@SQ SN:GL000211.1 LN:166566 M5:GL000211.1
@SQ SN:GL000244.1 LN:39929 M5:GL000244.1
@RG ID:SRR062634 SM:HG00096 CN:WUGSC DS:SRP001294 LB:2845856850 PI:206 PL:ILLUMINA
SRR062634.20563591 99 22 16050128 0 100M = 16050189 161 GGACAACATTCACCTTTAAAAGTTTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGFGGGGGEGGGGGGEFGFGGFGGGGFBGGGDE>EEECBCCEEC>E:A@=ADBCAB X0:i:2 X1:i:0 XA:Z:14,-19792774,100M,0; LB:Z:2845856850 MD:Z:100 RG:Z:SRR062634 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R
SRR062634.20563591 147 22 16050189 0 100M = 16050128 -161 GCAAGAAACTAAAGGGTCGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCA =DDFECDCFEDFEFFFEEFD:EF?FBFFFFBACEF?EGGGEDGGBGEGFGGGGGGFGGGGGGGGGFGGGGFFGGGGGGGFGGGGGGGGGGGGGGGGGGGG X0:i:2 X1:i:0 XA:Z:14,+19792713,100M,0; LB:Z:2845856850 MD:Z:100 RG:Z:SRR062634 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R
SRR062634.5613583 99 22 16050206 0 100M = 16050264 158 TGCAGGCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAATTATTTTCTTATTAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGA GGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGEFEGDCEEEBF?DDEEGDGEEEGE=ABB? X0:i:2 X1:i:0 XA:Z:14,-19792696,100M,2; LB:Z:2845856850 MD:Z:0C45A53 RG:Z:SRR062634 XG:i:0 AM:i:0 NM:i:2 SM:i:0 XM:i:2 XO:i:0 XT:A:R
SRR062634.5613583 147 22 16050264 0 100M = 16050206 -158 TAACTTCCTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGCTATCATTCATTTTCCTTGATTTGGGAGCCTAAT @E=EAEEEEGF?EEGEGFFEDBGEGFGGGGFGFFGFGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG X0:i:2 X1:i:0 XA:Z:14,+19792638,100M,0; LB:Z:2845856850 MD:Z:100 RG:Z:SRR062634 XG:i:0 AM:i:0 NM:i:0 SM:i:0 XM:i:0 XO:i:0 XT:A:R
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