基因数据处理51之cs-bwamem集群版运行*

将master的local改为集群就可以了。

集群运行结果：

问题：
匹配50条的时候，bwa和snap都是生成50条。但是cs-bwamem会生成492条，其中25和50条重读的很多，匹配位置不同。不知道为啥？

记录：

D:1win7javajdkbinjava -Didea.launcher.port=7538 "-Didea.launcher.bin.path=D:1win7ideaIntelliJ IDEA Community Edition 15.0.4bin" -Dfile.encoding=UTF-8 -classpath "D:1win7javajdkjrelibcharsets.jar;D:1win7javajdkjrelibdeploy.jar;D:1win7javajdkjrelibextaccess-bridge-64.jar;D:1win7javajdkjrelibextdnsns.jar;D:1win7javajdkjrelibextjaccess.jar;D:1win7javajdkjrelibextlocaledata.jar;D:1win7javajdkjrelibextsunec.jar;D:1win7javajdkjrelibextsunjce_provider.jar;D:1win7javajdkjrelibextsunmscapi.jar;D:1win7javajdkjrelibextzipfs.jar;D:1win7javajdkjrelibjavaws.jar;D:1win7javajdkjrelibjce.jar;D:1win7javajdkjrelibjfr.jar;D:1win7javajdkjrelibjfxrt.jar;D:1win7javajdkjrelibjsse.jar;D:1win7javajdkjrelibmanagement-agent.jar;D:1win7javajdkjrelibplugin.jar;D:1win7javajdkjrelibresources.jar;D:1win7javajdkjrelibrt.jar;D:1win7scala;D:1win7scalalib;D:allideagcdss-mastergcdss-clitargetscala-2.10.3test-classes;D:allideagcdss-mastergcdss-clitargetscala-2.10.3classes;D:1win7scalalibscala-actors-migration.jar;D:1win7scalalibscala-actors.jar;D:1win7scalalibscala-library.jar;D:1win7scalalibscala-reflect.jar;D:1win7scalalibscala-swing.jar;D:1win7javaotherJarspark-assembly-1.5.2-hadoop2.6.0.jar;C:Usersxubo.m2repositoryorgbdgenomicsutilsutils-cli_2.10.2.3utils-cli_2.10-0.2.3.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-avro1.7.0parquet-avro-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-column1.7.0parquet-column-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-common1.7.0parquet-common-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-encoding1.7.0parquet-encoding-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-generator1.7.0parquet-generator-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-hadoop1.7.0parquet-hadoop-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-jackson1.7.0parquet-jackson-1.7.0.jar;C:Usersxubo.m2repositoryorgapacheparquetparquet-format2.3.0-incubatingparquet-format-2.3.0-incubating.jar;C:Usersxubo.m2repositoryorgbdgenomicsutilsutils-misc_2.10.2.3utils-misc_2.10-0.2.3.jar;C:Usersxubo.m2repositoryorgbdgenomicsutilsutils-metrics_2.10.2.3utils-metrics_2.10-0.2.3.jar;C:Usersxubo.m2repositoryorgscala-langscala-library2.10.4scala-library-2.10.4.jar;C:Usersxubo.m2repositoryargs4jargs4j2.0.23args4j-2.0.23.jar;C:Usersxubo.m2repositoryorgbdgenomicsavocadoavocado-core.0.3-SNAPSHOTavocado-core-0.0.3-20160602.102034-3556.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-client2.2.0hadoop-client-2.2.0.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-common2.2.0hadoop-common-2.2.0.jar;C:Usersxubo.m2repositorycommons-clicommons-cli1.2commons-cli-1.2.jar;C:Usersxubo.m2repositoryorgapachecommonscommons-math2.1commons-math-2.1.jar;C:Usersxubo.m2repositoryxmlencxmlenc.52xmlenc-0.52.jar;C:Usersxubo.m2repositorycommons-httpclientcommons-httpclient3.1commons-httpclient-3.1.jar;C:Usersxubo.m2repositorycommons-codeccommons-codec1.4commons-codec-1.4.jar;C:Usersxubo.m2repositorycommons-loggingcommons-logging1.1.1commons-logging-1.1.1.jar;C:Usersxubo.m2repositorycommons-langcommons-lang2.5commons-lang-2.5.jar;C:Usersxubo.m2repositorycommons-configurationcommons-configuration1.10commons-configuration-1.10.jar;C:Usersxubo.m2repositorycomgoogleprotobufprotobuf-java2.5.0protobuf-java-2.5.0.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-auth2.2.0hadoop-auth-2.2.0.jar;C:Usersxubo.m2repositoryorgapachezookeeperzookeeper3.4.5zookeeper-3.4.5.jar;C:Usersxubo.m2repositoryorgapachecommonscommons-compress1.4.1commons-compress-1.4.1.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-hdfs2.2.0hadoop-hdfs-2.2.0.jar;C:Usersxubo.m2repositoryorgmortbayjettyjetty-util6.1.26jetty-util-6.1.26.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-mapreduce-client-app2.2.0hadoop-mapreduce-client-app-2.2.0.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-mapreduce-client-common2.2.0hadoop-mapreduce-client-common-2.2.0.jar;C:Usersxubo.m2repositoryorgapachehadoophadoop-yarn-client2.2.0hadoop-yarn-client-2.2.0.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-test-frameworkjersey-test-framework-grizzly21.9jersey-test-framework-grizzly2-1.9.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-test-frameworkjersey-test-framework-core1.9jersey-test-framework-core-1.9.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-client1.9jersey-client-1.9.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-grizzly21.9jersey-grizzly2-1.9.jar;C:Usersxubo.m2repositoryorgglassfishgrizzlygrizzly-http2.1.2grizzly-http-2.1.2.jar;C:Usersxubo.m2repositoryorgglassfishgrizzlygrizzly-framework2.1.2grizzly-framework-2.1.2.jar;C:Usersxubo.m2repositoryorgglassfishgmbalgmbal-api-only3.0.0-b023gmbal-api-only-3.0.0-b023.jar;C:Usersxubo.m2repositoryorgglassfishexternalmanagement-api3.0.0-b012management-api-3.0.0-b012.jar;C:Usersxubo.m2repositoryorgglassfishgrizzlygrizzly-http-server2.1.2grizzly-http-server-2.1.2.jar;C:Usersxubo.m2repositoryorgglassfishgrizzlygrizzly-rcm2.1.2grizzly-rcm-2.1.2.jar;C:Usersxubo.m2repositoryorgglassfishgrizzlygrizzly-http-servlet2.1.2grizzly-http-servlet-2.1.2.jar;C:Usersxubo.m2repositoryorgglassfishjavax.servlet3.1javax.servlet-3.1.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-json1.9jersey-json-1.9.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sjsr3051.3.9jsr305-1.3.9.jar;C:Usersxubo.m2repositoryorgslf4jslf4j-api1.7.10slf4j-api-1.7.10.jar;C:Usersxubo.m2repositoryorgslf4jjul-to-slf4j1.7.10jul-to-slf4j-1.7.10.jar;C:Usersxubo.m2repositoryorgslf4jjcl-over-slf4j1.7.10jcl-over-slf4j-1.7.10.jar;C:Usersxubo.m2repositorylog4jlog4j1.2.17log4j-1.2.17.jar;C:Usersxubo.m2repositorycomningcompress-lzf1.0.3compress-lzf-1.0.3.jar;C:Usersxubo.m2repositoryorgxerialsnappysnappy-java1.1.1.7snappy-java-1.1.1.7.jar;C:Usersxubo.m2repositorynetjpountzlz4lz41.2.0lz4-1.2.0.jar;C:Usersxubo.m2repositoryorgroaringbitmapRoaringBitmap.4.5RoaringBitmap-0.4.5.jar;C:Usersxubo.m2repositorycommons-netcommons-net2.2commons-net-2.2.jar;C:Usersxubo.m2repositoryorgspark-projectakkaakka-remote_2.102.3.4-sparkakka-remote_2.10-2.3.4-spark.jar;C:Usersxubo.m2repositoryorgspark-projectakkaakka-actor_2.102.3.4-sparkakka-actor_2.10-2.3.4-spark.jar;C:Usersxubo.m2repositorycomtypesafeconfig1.2.1config-1.2.1.jar;C:Usersxubo.m2repositoryionettynetty3.8.0.Finalnetty-3.8.0.Final.jar;C:Usersxubo.m2repositoryorgspark-projectprotobufprotobuf-java2.5.0-sparkprotobuf-java-2.5.0-spark.jar;C:Usersxubo.m2repositoryorguncommonsmathsuncommons-maths1.2.2auncommons-maths-1.2.2a.jar;C:Usersxubo.m2repositoryorgspark-projectakkaakka-slf4j_2.102.3.4-sparkakka-slf4j_2.10-2.3.4-spark.jar;C:Usersxubo.m2repositoryorgjson4sjson4s-jackson_2.103.2.10json4s-jackson_2.10-3.2.10.jar;C:Usersxubo.m2repositoryorgjson4sjson4s-core_2.103.2.10json4s-core_2.10-3.2.10.jar;C:Usersxubo.m2repositoryorgjson4sjson4s-ast_2.103.2.10json4s-ast_2.10-3.2.10.jar;C:Usersxubo.m2repositoryorgscala-langscalap2.10.0scalap-2.10.0.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-server1.9jersey-server-1.9.jar;C:Usersxubo.m2repositoryasmasm3.1asm-3.1.jar;C:Usersxubo.m2repositorycomsunjerseyjersey-core1.9jersey-core-1.9.jar;C:Usersxubo.m2repositoryorgapachemesosmesos.21.1mesos-0.21.1-shaded-protobuf.jar;C:Usersxubo.m2repositoryionettynetty-all4.0.23.Finalnetty-all-4.0.23.Final.jar;C:Usersxubo.m2repositorycomclearspringanalyticsstream2.7.0stream-2.7.0.jar;C:Usersxubo.m2repositoryiodropwizardmetricsmetrics-core3.1.0metrics-core-3.1.0.jar;C:Usersxubo.m2repositoryiodropwizardmetricsmetrics-jvm3.1.0metrics-jvm-3.1.0.jar;C:Usersxubo.m2repositoryiodropwizardmetricsmetrics-json3.1.0metrics-json-3.1.0.jar;C:Usersxubo.m2repositoryiodropwizardmetricsmetrics-graphite3.1.0metrics-graphite-3.1.0.jar;C:Usersxubo.m2repositorycomfasterxmljacksoncorejackson-databind2.4.4jackson-databind-2.4.4.jar;C:Usersxubo.m2repositorycomfasterxmljacksoncorejackson-annotations2.4.0jackson-annotations-2.4.0.jar;C:Usersxubo.m2repositorycomfasterxmljacksoncorejackson-core2.4.4jackson-core-2.4.4.jar;C:Usersxubo.m2repositorycomfasterxmljacksonmodulejackson-module-scala_2.102.4.4jackson-module-scala_2.10-2.4.4.jar;C:Usersxubo.m2repositoryorgscala-langscala-reflect2.10.4scala-reflect-2.10.4.jar;C:Usersxubo.m2repositoryorgapacheivyivy2.4.0ivy-2.4.0.jar;C:Usersxubo.m2repositoryorooro2.0.8oro-2.0.8.jar;C:Usersxubo.m2repositoryorgtachyonprojecttachyon-client.6.4tachyon-client-0.6.4.jar;C:Usersxubo.m2repositoryorgtachyonprojecttachyon.6.4tachyon-0.6.4.jar;C:Usersxubo.m2repositorynetrazorvinepyrolite4.4pyrolite-4.4.jar;C:Usersxubo.m2repositorynetsfpy4jpy4j.8.2.1py4j-0.8.2.1.jar;C:Usersxubo.m2repositoryorgspark-projectsparkunused1.0.0unused-1.0.0.jar;C:Usersxubo.m2repositoryorgapachesparkspark-sql_2.101.4.1spark-sql_2.10-1.4.1.jar;C:Usersxubo.m2repositoryorgapachesparkspark-catalyst_2.101.4.1spark-catalyst_2.10-1.4.1.jar;C:Usersxubo.m2repositoryorgscala-langscala-compiler2.10.4scala-compiler-2.10.4.jar;C:Usersxubo.m2repositoryorgscalamacrosquasiquotes_2.102.0.1quasiquotes_2.10-2.0.1.jar;C:Usersxubo.m2repositorycomtwitterparquet-column1.6.0rc3parquet-column-1.6.0rc3.jar;C:Usersxubo.m2repositorycomtwitterparquet-common1.6.0rc3parquet-common-1.6.0rc3.jar;C:Usersxubo.m2repositorycomtwitterparquet-encoding1.6.0rc3parquet-encoding-1.6.0rc3.jar;C:Usersxubo.m2repositorycomtwitterparquet-generator1.6.0rc3parquet-generator-1.6.0rc3.jar;C:Usersxubo.m2repositorycomtwitterparquet-hadoop1.6.0rc3parquet-hadoop-1.6.0rc3.jar;C:Usersxubo.m2repositorycomtwitterparquet-format2.2.0-rc1parquet-format-2.2.0-rc1.jar;C:Usersxubo.m2repositorycomtwitterparquet-jackson1.6.0rc3parquet-jackson-1.6.0rc3.jar;C:Usersxubo.m2repositoryorgjoddjodd-core3.6.3jodd-core-3.6.3.jar;C:Usersxubo.m2repositoryorgscalatestscalatest_2.101.9.2scalatest_2.10-1.9.2.jar;D:1win7ideaIntelliJ IDEA Community Edition 15.0.4libidea_rt.jar" com.intellij.rt.execution.application.AppMain org.bdgenomics.avocado.cli.parquetRead2csbwamemDup
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/D:/1win7/java/otherJar/spark-assembly-1.5.2-hadoop2.6.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/C:/Users/xubo/.m2/repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
2016-06-03 14:15:27 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2016-06-03 14:15:29 WARN  MetricsSystem:71 - Using default name DAGScheduler for source because spark.app.id is not set.
start:
2016-06-03 14:15:31 WARN  :139 - Your hostname,xubo-PC resolves to a loopback/non-reachable address: fe80:0:0:0:482:722f:5976:ce1f%39,but we couldn't find any external IP address!
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
2016-06-03 14:15:36 WARN  ParquetRecordReader:193 - Can not initialize counter due to context is not a instance of TaskInputOutputContext,but is org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl
+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
|              contig|    start|      end|mapq|readName|            sequence|                qual|cigar|basesTrimmedFromStart|basesTrimmedFromEnd|readPaired|properPair|readMapped|mateMapped|firstOfPair|secondOfPair|failedVendorQualityChecks|duplicateRead|readNegativeStrand|mateNegativeStrand|primaryAlignment|secondaryAlignment|supplementaryAlignment|mismatchingPositions|origQual|          attributes|recordGroupName|recordGroupSequencingCenter|recordGroupDescription|recordGroupRunDateEpoch|recordGroupFlowOrder|recordGroupKeySequence|recordGroupLibrary|recordGroupPredictedMedianInsertSize|recordGroupPlatform|recordGroupPlatformUnit|recordGroupSample|mateAlignmentStart|mateAlignmentEnd|mateContig|
+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
|[chr1,248956422,n...| 93465784| 93465884|  26| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|            true|             false|                 false|                 100|    null|NM:i:0    AS:i:100    X...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|101668921|101669021|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|231780491|231780591|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|              true|             false|           false|              true|                 false|              80C9C9|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...| 69447775| 69447875|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 71519060| 71519160|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|187344346|187344446|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|188353053|188353153|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|242097330|242097430|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|112217125|112217225|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|218009808|218009908|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|147407851|147407951|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 45962351| 45962451|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...| 47126825| 47126925|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|152431792|152431892|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|237080611|237080711|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 82131491| 82131591|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...| 69486875| 69486975|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...|224551051|224551151|   0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|154119974|154120074|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
|[chr1,n...| 78244128| 78244228|   0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M|                    0|                  0|     false|     false|      true|     false|      false|       false|                    false|        false|             false|             false|           false|              true|                 false|              9G9G80|    null|NM:i:2    AS:i:90 RG...|            foo|                       null|                  null|                   null|                null|                  null|              null|                                null|               null|                   null|              bar|              null|            null|      null|
+--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+
only showing top 20 rows

2016-06-03 14:15:37 WARN  ParquetRecordReader:193 - Can not initialize counter due to context is not a instance of TaskInputOutputContext,but is org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl
492
2016-06-03 14:15:38 WARN  ParquetRecordReader:193 - Can not initialize counter due to context is not a instance of TaskInputOutputContext,but is org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl
1:[[chr1,null,null],93465784,93465884,26,chr1-50,TTCCACAATAGTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA,@@CDFDFDHFHGHIJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,DCC<CEFD<EDDCD,100M,0,false,true,100,NM:i:0 AS:i:100    XS:i:90 RG:Z:foo,foo,bar,null]
2:[[chr1,101668921,101669021,9G9G80,NM:i:2 AS:i:90 RG:Z:foo,null]
3:[[chr1,231780491,231780591,TTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAATTAGTTCAACTATTGTGGAA,DCDDE<DFEC<CCD,D8DCFHDDHCADDAF85DD@&@3IG=HEHFFGCIIC(8GH)(JHBGIJGF@BIJEDIDJ?EJJ(JJJI:HJIHGHFHDFDFDC@@,80C9C9,NM:i:2  AS:i:90 RG:Z:foo,null]
4:[[chr1,69447775,69447875,NM:i:2    AS:i:90 RG:Z:foo,null]
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13:[[chr1,47126825,47126925,NM:i:2   AS:i:90 RG:Z:foo,null]
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274:[[chr1,159265478,159265578,null]
275:[[chr1,73291918,73292018,null]
276:[[chr1,79889139,79889239,null]
277:[[chr1,221383641,221383741,null]
278:[[chr1,172981857,172981957,null]
279:[[chr1,237020046,237020146,null]
280:[[chr1,121310004,121310104,null]
281:[[chr1,34097744,34097844,null]
282:[[chr1,108494511,108494611,null]
283:[[chr1,228521270,228521370,null]
284:[[chr1,30454168,30454268,9G9T80,null]
285:[[chr1,20907974,20908074,null]
286:[[chr1,223318438,223318538,null]
287:[[chr1,36758790,36758890,null]
288:[[chr1,191063866,191063966,null]
289:[[chr1,207721772,207721872,0A8G9G80,NM:i:3 AS:i:89 RG:Z:foo,null]
290:[[chr1,86673348,86673448,80C9C7G1,NM:i:3    AS:i:88 RG:Z:foo,null]
291:[[chr1,63037532,63037632,1C7G9G80,NM:i:3   AS:i:88 RG:Z:foo,null]
292:[[chr1,85825504,85825604,null]
293:[[chr1,112226757,112226857,80C9C7T1,NM:i:3  AS:i:88 RG:Z:foo,null]
294:[[chr1,102534581,102534681,80C9C6A2,NM:i:3  AS:i:87 RG:Z:foo,null]
295:[[chr1,102504761,102504861,2T6G9G80,NM:i:3 AS:i:87 RG:Z:foo,null]
296:[[chr1,147449761,147449861,null]
297:[[chr1,7598516,7598616,3T5G9G80,NM:i:3 AS:i:86 RG:Z:foo,null]
298:[[chr1,7214189,7214289,null]
299:[[chr1,66806109,66806209,80C9C5A3,NM:i:3    AS:i:86 RG:Z:foo,null]
300:[[chr1,199607148,199607248,80C9C2G6,NM:i:3  AS:i:85 RG:Z:foo,null]
301:[[chr1,14048851,14048951,5T3G9G80,NM:i:3   AS:i:85 RG:Z:foo,null]
302:[[chr1,233043988,233044088,8G0G9G80,NM:i:3 AS:i:85 RG:Z:foo,null]
303:[[chr1,85647342,85647442,80C9C0C8,NM:i:3    AS:i:85 RG:Z:foo,null]
304:[[chr1,69905838,69905938,null]
305:[[chr1,102643782,102643882,80C9C1C7,null]
306:[[chr1,211402872,211402972,9G2C6G80,null]
307:[[chr1,59648329,59648429,9G0T8G80,null]
308:[[chr1,60645355,60645455,80C9C0G8,null]
309:[[chr1,180761602,180761702,null]
310:[[chr1,186642678,186642778,null]
311:[[chr1,46808225,46808325,9G0A8G80,null]
312:[[chr1,168660144,168660244,6C2G9G80,null]
313:[[chr1,202467804,202467904,9G1C7G80,null]
314:[[chr1,73239991,73240091,80C9C3T5,null]
315:[[chr1,38470208,38470308,null]
316:[[chr1,86162930,86163030,5G3G9G80,null]
317:[[chr1,152835696,152835796,null]
318:[[chr1,42814699,42814799,80C9C3A5,null]
319:[[chr1,71220648,71220748,80C8T0C9,null]
320:[[chr1,108162374,108162474,null]
321:[[chr1,79938968,79939068,6T2G9G80,null]
322:[[chr1,169639988,169640088,null]
323:[[chr1,96241356,96241456,7G1G9G80,null]
324:[[chr1,215537691,215537791,null]
325:[[chr1,193804103,193804203,80C2C6C9,null]
326:[[chr1,93402538,93402638,null]
327:[[chr1,114183207,114183307,9G7C1G80,null]
328:[[chr1,105948470,105948570,null]
329:[[chr1,76915174,76915274,80C9C2C6,null]
330:[[chr1,46663363,46663463,null]
331:[[chr1,47171386,47171486,80C7T1C9,null]
332:[[chr1,246525720,246525820,80C7C1C9,null]
333:[[chr1,147460920,147461020,null]
334:[[chr1,79511839,79511939,null]
335:[[chr1,158241978,158242078,80G9C2A6,null]
336:[[chr1,45290030,45290130,null]
337:[[chr1,58770759,58770859,9G3C5G80,null]
338:[[chr1,168884590,168884690,9G3A5G80,null]
339:[[chr1,169604031,169604131,null]
340:[[chr1,172244686,172244786,80C7G1C9,null]
341:[[chr1,182005904,182005994,GTTGAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA,HGHIJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,10H90M,10,9G80,NM:i:1  AS:i:85 RG:Z:foo,null]
342:[[chr1,166750019,166750119,null]
343:[[chr1,98212632,98212732,null]
344:[[chr1,152273377,152273477,null]
345:[[chr1,242618083,242618183,80C0G8C9,null]
346:[[chr1,58269603,58269703,null]
347:[[chr1,117831599,117831689,null]
348:[[chr1,25512037,25512137,null]
349:[[chr1,76458216,76458316,null]
350:[[chr1,230298465,230298565,null]
351:[[chr1,105943889,105943989,null]
352:[[chr1,55127648,55127748,null]
353:[[chr1,89961189,89961289,80C0A8C9,null]
354:[[chr1,218560999,218561099,null]
355:[[chr1,49658339,49658439,80C1C7C9,null]
356:[[chr1,103020169,103020269,9G6A2G80,null]
357:[[chr1,59538325,59538425,80C5G3C9,null]
358:[[chr1,246329271,246329371,9G1G7G80,null]
359:[[chr1,225212486,225212586,null]
360:[[chr1,60379386,60379486,8C0G9G80,null]
361:[[chr1,33891380,33891480,null]
362:[[chr1,74882473,74882573,null]
363:[[chr1,73450148,73450238,TTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAATTAGTTCAAC,D8DCFHDDHCADDAF85DD@&@3IG=HEHFFGCIIC(8GH)(JHBGIJGF@BIJEDIDJ?EJJ(JJJI:HJIHGH,90M10H,80C9,NM:i:1 AS:i:85 RG:Z:foo,null]
364:[[chr1,47086274,47086374,9G1A7G80,null]
365:[[chr1,174843808,174843908,9G8G0G80,null]
366:[[chr1,89413161,89413261,4G4G9G80,null]
367:[[chr1,115626313,115626413,5A3G9G80,null]
368:[[chr1,106168730,106168830,80C8T0C1C7,NM:i:4    AS:i:84 RG:Z:foo,null]
369:[[chr1,118496869,118496969,80C8T0C2G6,null]
370:[[chr1,96279177,96279277,7G1G1C7G80,NM:i:4 AS:i:83 RG:Z:foo,null]
371:[[chr1,99338548,99338635,GAACTAATTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA,IJH:IJJJ(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,13H87M,13,6G80,NM:i:1  AS:i:82 RG:Z:foo,null]
372:[[chr1,87668495,87668597,85M2D15M,80C4^TC5C9,NM:i:4  AS:i:82 RG:Z:foo,null]
373:[[chr1,4704737,4704837,6G2G3A5G80,NM:i:4   AS:i:81 RG:Z:foo,null]
374:[[chr1,58373759,58373859,6G2G3C5G80,NM:i:4 AS:i:81 RG:Z:foo,null]
375:[[chr1,189760272,189760372,80C1G7C0C8,NM:i:4    AS:i:80 RG:Z:foo,null]
376:[[chr1,158388093,158388173,TTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA,D8DCFHDDHCADDAF85DD@&@3IG=HEHFFGCIIC(8GH)(JHBGIJGF@BIJEDIDJ?EJJ(J,80M20H,20,80,NM:i:0 AS:i:80 RG:Z:foo,null]
377:[[chr1,178897268,178897348,null]
378:[[chr1,49515369,49515469,80C1C0A6A9,NM:i:4  AS:i:80 RG:Z:foo,null]
379:[[chr1,198871943,198872043,9G4C2C1G80,NM:i:4   AS:i:80 RG:Z:foo,null]
380:[[chr1,189091946,189092046,9G0A6C1G80,null]
381:[[chr1,99563769,99563869,80C0A3C4C9,null]
382:[[chr1,153443173,153443253,null]
383:[[chr1,103795714,103795814,9G72C0A3T12,null]
384:[[chr1,209973811,209973891,TTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAA,J(JJE?JDIDEJIB@FGJIGBHJ()HG8(CIICGFFHEH=GI3@&@DD58FADDACHDDHFCD8D,20H80M,NM:i:0    AS:i:80 RG:Z:foo,null]
385:[[chr1,98543154,98543234,NM:i:0  AS:i:80 RG:Z:foo,null]
386:[[chr1,223367117,223367217,9G7G0G0G80,null]
387:[[chr1,228133745,228133845,60,chr1-48,ATCATTGTATGCCACAGAAATAATTAAATTTCCTTGTCAACTGACACATTATTATTAGGCACTCTCACCAGATCTTTACCCATGGCCATTTAAAGTGTGG,@>CFFFFFH<<GC1IIDCFJJHIGIHJ(IID7IJ,FJJJHJJJJ)GGBHIJFJFIFIHFE=HEIEE;CA)G0(D()HC@D(:EFDDC@;DDAC95(D?BD,44G55,NM:i:1   AS:i:95 XS:i:0  RG:Z:foo,null]
388:[[chr1,13772987,13773087,chr1-47,TTCAGTAATTCAGAATAACACATGAGGGAATGAATGAATGAATAAATAAAAAAAAACTGAATGAATAAATTACAAAAAATTGTGTTTCAGGGAAGAAAAA,CC@F(FFFDFH.HDHIGI(JIIIGGIEEJIIIHJJHHH3IJJIIJ3=EI>JDIGH((IBJCIEHGD>;J@HF+DC)CCCADBDBD+BDDDD5B5DDDE(C,56A15A27,NM:i:2  AS:i:90 XS:i:19 RG:Z:foo,null]
389:[[chr1,37474757,37474857,chr1-46,GGGTCGGGGTCCTGTTCCCCGGTCCGCCGGGCCTCAGGACCCCTCCAACTTTGCCCAAGTTGGGAGAGCCGGGGAAGAGCACCAGGTTCCTGATCGGGAT,(5CBACDDD>FBDDDDDEC:CE(CBDFDDHEFH;FGEFHGHDGJJJDIGI:JEHJ=JJJJJH8CI?JJJG9JIII>IJIIGJ=EIJGAHHHHFFDFDCC?,22C77,NM:i:1  AS:i:95 XS:i:0  RG:Z:foo,null]
390:[[chr1,29056656,29056756,chr1-45,CTGGGATTACAGGTGCCCGCCACCATGCCCAGCTAATTTTTGTATTTTTGGTAGAGACAAGGTTTCACCATGTTGGCCGGGATTGTCTCGAACTCCTGAT,B@@FFFFFHHG)HIJJJJBJIJCJHGJIBFJJI3IIHDF@JIAJ9JJJIJJBIJJ?BJID8F:HFHA(+D>J>CG>7D=DDFF@EDC3D<CDDDC@BD@B,NM:i:0   AS:i:100    XS:i:0  RG:Z:foo,null]
391:[[chr1,49993892,49993992,chr1-44,CAATTTAGCCAAAACTGGCTAATCGTTTTACCAGAATCATTCCCATTGTTCAAGACCTATTTTAAGCTCCACTATCACCATAAAACTTTCCCGATCAGTT,C@CFFFFDHHHHH<IEJJ@JJJHI)IDIBIJA:HJHFJJJIJGGJJIIIIHGGJJGH<(IIIJI?ICDG;CDHFHCDCCB?FDDED:CD:>DD5C&DDCD,24C75,NM:i:1 AS:i:95 XS:i:0  RG:Z:foo,null]
392:[[chr1,194714505,194714605,chr1-43,AATATGTTTTAATAATATCATATTTAAATTTGATGATACTTTAAAAATGGTTCCATGTGTGTTCTCTTGGGTTATTTCACAATCAATAAAAGGTCTGCAA,CCCCDDC@E>CDCDDC>D9CD=C)CGC>E@7.HF)DIBJBJJ.JEJEJ@JJIIIIGD?<IHH)FJJIIH*DJIBIIJHJIHHJFHIGHHHHDFDFDFC@B,NM:i:0  AS:i:100    XS:i:0  RG:Z:foo,null]
393:[[chr1,35706202,35706302,41,chr1-42,CAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCACGTGCCACCATGCCTGGCAATTTTTGTATTTTTAGTACAGATGGGG,CC@FDFFAHHGFHJIHJFJJII=@JEHIJIIJIJEJIJJHHGIJBBFJG6JJHJJG<F3JJHIFG(DCJDHDFDCHDDF7DDHBDFDDCDDCDCD;CBCB,NM:i:0   AS:i:100    XS:i:84 RG:Z:foo,null]
394:[[chr1,93072855,93072956,CCCCATCTGTACTAAAAATACAAAAATTGCCAGGCATGGTGGCACGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTG,BCBC;DCDCDDCDDFDBHDD7FDDHCDFDHDJCD(GFIHJJ3F<GJJHJJ6GJFBBJIGHHJJIJEJIJIIJIHEJ@=IIJJFJHIJHFGHHAFFDF@CC,28M1D72M,4G3C19^A72,NM:i:3  AS:i:84 RG:Z:foo,null]
395:[[chr1,156482337,156482437,chr1-41,GTGTGTGCATAGGCAGGTCTGCGTGTACATGCAACGTGGGCACGTGTCCATGTGGATGCAGGCGGGGGTATATCCTGGTGCCTGTGTGTATGGGCCCACC,D;CCDDCDCDDDCD:EDA@<C<E(GDDDGDJDDHJ@CJJI,=FHJJIGJ7GEC?IGJJIFBBICHJEIJJHHAIJIJI.IJGJJGJJHHGHHFFFFFB=B,null]
396:[[chr1,221779283,221779383,chr1-40,CATGGCACATAGCACTTTGGTGATGGGGACTGCTTTGCTAATGTCAGGGTCAAGGGGTGCATGGACCATGGGCAGAGTGCTGGGCTCAGCCAAATGGTTC,DDBCDCDDDDDDD25F?DD@4I5HED?CAHGA?JJIIJB)IHFJJFCJII?@<HIIFGIJIJFG?JIJCIIJJ)IJJIJIJJIIEGJFHHHFFDFDFC@@,39G60,NM:i:1    AS:i:95 XS:i:0  RG:Z:foo,null]
397:[[chr1,3895604,3895704,chr1-39,GTCCTCTCCGGATTGACAGGAGTCAAAACATGAGATCGGCTTAGCTTCAGTTTCGTCATGGATTAACCACCTCCAAGGTGTCAACTCCAAAATGTCAAGA,DD5CCAD&8DAD>D&FDDDCDBDD?6DD.FHDDIFE?@IDEGIBCGD?JFJ>JGBI,IJIF.JJIHJJJEIEGFJ=JJHJHHJFHIJHHHHHFFAFFC@B,null]
398:[[chr1,33174925,33175025,chr1-38,CACACATACATATATGTGTGTATATATATATATATATATATATACACACATATACATATATATGCACACACACATGTATGTATATGTATATGTATATGTG,CDDC(FBDC(AACBDDCBDDECEC5@H;HFDJFH>=FCHAHJFJ'H3JG9JFEHIJFDJJ9IJHEJIGJIJJJJJC;J?AJFJGEHFHDC<HDFFFDCC#,99A0,NM:i:1   AS:i:99 XS:i:24 RG:Z:foo,null]
399:[[chr1,206124776,206124876,chr1-37,TCAGTCAATAGACATTTGGGTTGTTTCCACCTTGGGCAGGTTACAAATAATGCTGCTAGTGAACATTCATGTGCAAGTTTTTGTGTGGACATACGTTGTT,CBCD8DDADC@DDDDB?CCHD;@AHECEEJIHAEII?E05GFJHHDJCJEJDBHJE7GJJJGJGGGJ=JIC(JIJHHIIIAGGJIIICHGHGFFFDF?CC,null]
400:[[chr1,181673625,181673725,chr1-36,TCCACTGCCCAGAAAGAGGACATCCCTTATAGGACCAGCGGATGGAAGCCATGGGCTGGGCAGGACATTCCTGTCCCAACCCACATGGCAGCTAGAGTCC,@@3DFFFFHHHFHJJIGGJHHFJJJIIJJJJDH*GJJJGJIJ6AIJIJDFDII=HFI2AH1AIEAAC?JEIEDJF.HDH@FAFDCDE2D:DDBD0DDBDD,33G66,null]
401:[[chr1,152104779,152104879,chr1-35,ACCTCTATAAATACAATATCTTCAAATATGATTACATTCTGAGGTACTGAGGGTTAAGACTTCAACACGTGAACCTCTGTGGGGGTTGGGAGGTCACAAC,+@?D>>D?DDBDFB)DDDDDC5(9>F;G)FB84/AJE3JJIJIGIGJBBIGCJCJGJGHJIDJ>IB7IGJGEGCIIGFJJJEFHIIJHHF=HFF8=F??=,14C85,null]
402:[[chr1,12934212,12934312,chr1-34,TTTTGATACTTTTGATGTGGCCAAAGGTTCTCCAATAAAGATACCATATATAAATATATGTATTTCTAATGTCTGAAACAGATTAAAACCTTCCCTGTAT,D@CB?DEDCEDDD(DC>F>DEHE>HEDE@HDD.IDD3'5I8IBFJHDI=CIIJ8JFHIBJJI0IJGFFJGIIJJABH<)IFJJJIEDHHHHAFFFFFCC@,NM:i:0 AS:i:100    XS:i:100    RG:Z:foo,null]
403:[[chr1,13267476,13267576,ATACAGGGAAGGTTTTAATCTGTTTCAGACATTAGAAATACATATATTTATATATGGTATCTTTATTGGAGAACCTTTGGCCACATCAAAAGTATCAAAA,@CCFFFFFAHHHHDEIJJJFI)<HBAJJIIGJFFGJI0IJJBIHFJ8JIIC=IDHJFBI8I5'3DDI.DDH@EDEH>EHED>F>CD(DDDECDED?BC@D,NM:i:0    AS:i:100    RG:Z:foo,null]
404:[[chr1,48968232,48968332,chr1-33,TAATAGTAGGCAATAAACAAAGAGAGCAACTTAGGAGCCAGATCACATGTGGCCGCTCGAGCAATATGGTAAAAGTTCTGGACTTCATTCTAGGTGAATG,1CCB=FFFHHHHHEDHJIIAFG4JIFJIJB)JJI?(&JJIJJEE)HIJJBJ?HJ(=B(I@?I?8DC8C>JHJH>@EDFDD5DDDDDDDDCFD:=DCC(DD,0G53T45,NM:i:2   AS:i:94 XS:i:0  RG:Z:foo,null]
405:[[chr1,88980622,88980722,chr1-32,TAGTTCAGTAAACTATTTATCAAACAGGTGTCAGGTCATTTTAACATACTCCTTGCTTTGAACAATATTCATTCATACTTGGTACAAACTCTATATCCTA,B?CFDFFFHHFH3JIJJJIGJJJJJFJDEJGJ(EHFI>E=JIJ(GGJDFCH>>GJ=IHDJEHHDI>GEBJE@DD@HH'AA@ECC@BDEDDD@CDDADBDD,32T44T22,NM:i:2  AS:i:90 XS:i:0  RG:Z:foo,null]
406:[[chr1,227005593,227005693,chr1-31,TCACCAGGCATCTTTACTGACTCACACCAATAGTAGTACTGGGATTAGAAATAAGACGCTGCAATACTCACAACCTAGGTGAAGTTAGTTAATTTGGGAA,D@D5B=DACDDDDDBEFECBFDC5BCDDDCDFIDC8ICEIJ=DHIGHIJIJJB0HJJCDJHJGJIJI9GGHGGJ3@IJJAIJGGBGJ7HFHHDEBFF@CC,null]
407:[[chr1,9852128,9852228,chr1-30,TGTGAAATGGAGTCAGCAGAGTGAGCCGGCCTCCACTCAGTGAGCCGGGTCTCCCCCACAGCCGGCATGTGCTGACCTCCTTCCAACTGCTCTACCAAGA,CBCDDFFDHGHHHIEJ+J<EFJIJIIJI><J(IIFJG)0JGIJ?8J5;J?D@9IJHDI=DI)DDHG@3FAI5FF?EDAHDC@DDGD3AA>D+?ECDDDDB,NM:i:0 AS:i:100    XS:i:0  RG:Z:foo,null]
408:[[chr1,156397430,156397530,chr1-29,TCAGCCTCCCGAGTAGCTGGGATTACAGGAACCTGCCACCACGCCCGGCTAATTTTTGTATTTTCAGTTGAGACGGGGTTTCACCATGTTGCCCAGGCTG,D1D(@9DDDC@D0C3=CDDJ;FDHDD@H2BDHIDAGDDDCDIFJ9GIFGIG@?)JJHJGFGJIB7JG>'IJIJJGJ+JJGIIHFIJIDHHHFFFFFFC@B,68A31,NM:i:1    AS:i:95 XS:i:55 RG:Z:foo,null]
409:[[chr1,60314002,60314102,8T0G9A9T0G2C5T2A48A8,NM:i:9    AS:i:55 RG:Z:foo,null]
410:[[chr1,56986637,56986737,51,chr1-28,ACTCAGAACAGGTCTCCTTGTGGAACCATGGCCTTCCTTTTGGATCCTGGCCATGAGAGCCCATTCTTAGGAACCATGTTTCAATTCCAGTAGGTGATGT,DD)DC@C<EDDD+DC0BDDBDDCECFDIJJ@)?HDACJGDFI?JGJH)JJJJJIEIJIIJJGIJIHIJHJCIGDHI>J@A)GIFJJJHHFFHFDDFFCCC,NM:i:0    AS:i:100    XS:i:80 RG:Z:foo,null]
411:[[chr1,56983537,56983637,ACATCACCTACTGGAATTGAAACATGGTTCCTAAGAATGGGCTCTCATGGCCAGGATCCAAAAGGAAGGCCATGGTTCCACAAGGAGACCTGTTCTGAGT,CCCFFDDFHFFHHJJJFIG)A@J>IHDGICJHJIHIJIGJJIIJIEIJJJJJ)HJGJ?IFDGJCADH?)@JJIDFCECDDBDDB0CD+DDDE<C@CD)DD,10T59T0G9G18,null]
412:[[chr1,172015197,172015297,chr1-27,AGGTGTCAGTCCTCCAGCTTTGTTCTTCTTTTATATTGTGTTGGCTATCCTGGGCTCTTTGCTTCTCCATACAAAACTTAGAATCAGTTTGTTGATATCC,B8BD>/D<BED@CCEBBEBCH,F?CCD.E;HGJBJ)IGD7HED5@6JJJCHIGHJIJFDJCIJJHGJIJJJIEF:FEJHBJ.JJJIGHBHCF2DDFFCC@,null]
413:[[chr1,233336762,233336862,chr1-26,AGATATACAGCAAAGTTTGAAAGCTACAGTTCTGAGGACCATATTTATGGATTCCTTCTTATATGTTATCTGGGTTGATATAGAAATTCTTCCATGGCTA,CBCFDFF<H<G?AIBJJJGIEJIJIIJIIJJEGHEIJIIGI)GJHIJGF8JIIHED=DJH?IJFB;>;HHDDHHB?C9DE?DCE@D?B&5E>DDD7DD?D,41G58,null]
414:[[chr1,33891275,33891375,chr1-25,CAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGC,DDD>=D6FCDC?DDCDECHAEDD?DJIDE(EFE;:?DDG?JHJ>J3IIIHJHIHDEGJJJHHIGJIICH)GJIJIGIAJ:JFGICHHHHHGBFFFFDCCC,null]
415:[[chr1,152937577,152937677,GCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGCATTTTTTCATGTGTTTTTTGGCTG,CCCDFFFFBGHHHHHCIGFJ:JAIGIJIJG)HCIIJGIHHJJJGEDHIHJHIII3J>JHJ?GDD?:;EFE(EDIJD?DDEAHCEDCDD?CDCF6D=>DDD,NM:i:0  AS:i:100    RG:Z:foo,null]
416:[[chr1,105822717,105822817,NM:i:0   AS:i:100    RG:Z:foo,null]
417:[[chr1,224799703,224799803,null]
418:[[chr1,189760167,189760267,null]
419:[[chr1,60645250,60645350,NM:i:0 AS:i:100    RG:Z:foo,null]
420:[[chr1,166494340,166494440,null]
421:[[chr1,76458111,76458211,null]
422:[[chr1,96609612,96609712,null]
423:[[chr1,75682982,75683082,null]
424:[[chr1,178315475,178315575,null]
425:[[chr1,185379286,185379386,null]
426:[[chr1,90057972,90058072,null]
427:[[chr1,108162479,108162579,null]
428:[[chr1,170108163,170108263,null]
429:[[chr1,73291813,73291913,null]
430:[[chr1,38666940,38667040,null]
431:[[chr1,231593346,231593446,null]
432:[[chr1,159293945,159294045,null]
433:[[chr1,163750917,163751017,null]
434:[[chr1,202936969,202937069,null]
435:[[chr1,174694885,174694985,null]
436:[[chr1,96381477,96381577,null]
437:[[chr1,75839895,75839995,null]
438:[[chr1,184800050,184800150,null]
439:[[chr1,180389687,180389787,null]
440:[[chr1,105578658,105578758,null]
441:[[chr1,248258090,248258190,null]
442:[[chr1,196781487,196781587,null]
443:[[chr1,46017544,46017644,null]
444:[[chr1,65450962,65451062,null]
445:[[chr1,34097639,34097739,null]
446:[[chr1,112340661,112340761,null]
447:[[chr1,25060270,25060370,null]
448:[[chr1,143752554,143752654,null]
449:[[chr1,80950764,80950864,null]
450:[[chr1,195156618,195156718,null]
451:[[chr1,105787068,105787168,null]
452:[[chr1,196369946,196370046,null]
453:[[chr1,42494732,42494832,null]
454:[[chr1,113601448,113601548,null]
455:[[chr1,96853884,96853984,null]
456:[[chr1,69996089,69996189,null]
457:[[chr1,248025325,248025425,null]
458:[[chr1,74787817,74787917,null]
459:[[chr1,243661932,243662032,null]
460:[[chr1,194259938,194260038,null]
461:[[chr1,219948985,219949085,null]
462:[[chr1,4245072,4245172,null]
463:[[chr1,157610484,157610584,null]
464:[[chr1,112155481,112155581,null]
465:[[chr1,98543239,98543339,null]
466:[[chr1,235841968,235842068,chr1-24,GTTGGCTACTAGCTTAGCAGAGGTGCAAAACCATGAATTTCTGGTGGTATGGATTTTTTCAGCTATTTCAGATTCACCAGCAGGATCCAGCTGCTTGGGT,CCCFF?FFFHHHFGI,JEJIIG<JJ)I1GJG=ICJJEGJIJF<@IIBDJJIFDIEAIJB;JGADHJD,CBD@DEC;?DDHD<BEED&DD@DCDEDDDAD?,25G60T13,NM:i:2    AS:i:90 XS:i:0  RG:Z:foo,null]
467:[[chr1,96545357,96545457,chr1-23,AGTGAAAAAGGCTGGCTGCCCTTCAATATCATCTTCAAATGTTAACAACACTGAATATTAATAAATTTCCTTTAGCGAATAATGAATCCAGCCTTCCTTA,C@CF+FFFGGDHGJIBDJI2JGJIHHJJII?GJJJJGIJIJJGFJJG)IJ0HD0JIFJDJDFC;D7JGFFCEDFHADCDCCDEDDEAHDDD+9?<CA2:D,null]
468:[[chr1,80270678,80270778,chr1-22,TTGTACACCCTATTTCTGACCAGAAGAAGGAGCATTTTGCTTTTTGCCAAATGAGAAGTGCATTCTGGAAACACTTGATGCCTGCACCACACCTCGAGTT,?@CFDDFFHFHHHJJJGC7J(GI8IJJJE?HHI>BJG*IJFJIDJHD0IEJIHDI>@H=EHGIAHJ33(EJCDEDA?FDG<ADDDCDDEF9DDDD@DDBD,null]
469:[[chr1,35923260,35923360,chr1-21,CTAAGCAGCAGTGTTTTTGGATACTTTTTTTTTCTGTTTGTGAATAAGGCCAGCACTCAAGATGGGCAGCCAAGGGTGCACTGACTATTAGCTGGCCCAT,=@@DFDFEHGHHH8JIJGJH1JJHHJIHJGH?IIFEJIIG87JI=IAJJJBJIJD(IIFI8JIHF=JDHEJHEHDDCEDCDEACDDCCAD<BDE+B8(DD,null]
470:[[chr1,112489189,112489289,chr1-20,AGGGAATGAACTATGCACATCTATATAGTAACAGGGACAGATTTTTTTTTAACATGAGAGTGTAAAAAAAAGAAAAAGAAAAAAAAAGGCCAGGCACAGT,DACDABD@DDDDDA7DDDC8GHI@EI(DC?FG'+8.FBDJIHIEGG=IIG=I@*DFIJJIBIIJIJIIHJCHBGFJJJI@F>HJIIIHHAHFAFDFFC@1,33A66,NM:i:1    AS:i:95 XS:i:19 RG:Z:foo,null]
471:[[chr1,160371243,160371343,chr1-19,AGGCCCTGGGCACAGGCAGAGAGCCCACCGGCTGGTCATGAGGGCCTCTTCCTTTCTCTGACCCAGGCACCTCGAGGGCTCTTCTCCTGGGTTCCTTCCG,@@:FDDFFCHHAHI:GEJFJGF@JJJFIC9JIIJJJ?IIEFHGJ'G?BFFBIIDIG,J)AJIHEGFBHCI&ECCD@EDD?)DED(D>3C?ABEEDDD4BD,80A19,null]
472:[[chr1,179855834,179855934,chr1-18,AGCAATTAAAATAAATTAGGGTATCTTTAAAAGTTGTAAAATTATAGCAGTGAAGTACTGTTGACCAGGCACAGTGGCTCACACCTGTAATACCAGCACT,DCEDBBDD/DD9DDD@DDFB(DDDHCHDF;C?;FJGC/IJ8DHEJ:DFGGIGHBIGIJDI(JDHGJJGJIHJII@HJJJ3JIJDIJBBHHFHFDFFF@C@,20T39C39,NM:i:2 AS:i:90 XS:i:34 RG:Z:foo,null]
473:[[chr1,207455994,207456094,chr1-17,GGTTCTTATGATTGGAAAGGTTAAAGAGTGACCTATAGGTCACTTTCCAATTATGAAAACAAAAAATTAAGAAATATATATATTTTCATTATTTCACTCC,<DC>CBDDDCDD:&DDCFCFDDHDEJEDCFDJ;;EHGCD;CG?DIHGGCIJJJJ-GIJ7GIFHHHCGI)JJJJIJEGJIGJJJIH<GFGHHBFD@FDCC1,null]
474:[[chr1,114154602,114154702,chr1-16,TGTATCTTTCTGCTAAGCATAACAAGAAAGACAGAAAGCTCAACGGGAGGATTGAGGCTAGACTTAAAGTAGAGATCCCCTCAGAAACTGTGGAGTGAGG,CCCF8FFDHHHH4JIJIGIJIIFJHJJ?JEDI9BG?I>GHJ7FJJJIF67EIIHD2C>?>DDHDE8E7@JEJ(IFDDC;EDCC:FD>@DBC>D5D>=<AB,null]
475:[[chr1,169767579,169767679,chr1-15,GGTGGGGGAGAGGAAAGGAAACGAGGGAGGAAAGGCCCTAATAGGGAGGATTTTGGAGTTTAGATTTTAAAATGATAAAGGTTGTTTGACACTCTAGGCA,DEDD9DDD@DD4DDDAEDDDC@D7=D;DA)7;IIJFD(J?JJDGI(IDGD7D'3JIE;H?AC@EHJJE?JJHDFJIIIECG)GGJJECHFHHFDFDFC@C,45A35A18,NM:i:2 AS:i:90 XS:i:19 RG:Z:foo,null]
476:[[chr1,117644125,117644225,chr1-14,GCATTTCATTGTGGACTAATTTTCCCCCACTATTGAGGGAAGACCCTTTTGAGTACTCTATCTGATGCCCCATGAATGATAAAGTTTTATACTCTGGCTG,C?CFBDFFGHHH<JAGCIJJIIIGJJI8:JIJC(JGGJBJH-GIJIJJ;IIH;>JI5CJ=CD9DC-HGIJDCJHHDBEDDCC&DDDBD39DBCDDDDDCD,null]
477:[[chr1,104996993,104997093,chr1-13,TTCTTGCTGGAACACATGTTTTCACCTTTACCTTCACCCACAGCCCAATGTGCATCAATATGGAGATAATGCAGTTCCATTTATACCTCTTTGTGGTTCA,=@?FFFDDHBHHHJHJIJ)JIJ<IJII++>HBHIJ*G:CJCJJJI?G)>GJI;JD3FJ8FJFGD;DDDDFBED7C<?E@C>7&A(ABC9CD+DCC&DDCA,18G63G12A4,NM:i:3  AS:i:85 XS:i:22 RG:Z:foo,null]
478:[[chr1,108617704,108617804,chr1-12,AGGTCGGGGAGATTGGGAAGAAGAATGAGCAAAGAAACCACCAGTGTGATCAGAGGAGGAAAGCAAAGCAGAGTCCTGTCCTGAAAACCAAATGAAGAAA,:=>+D(DCEC=@GHB(CDDDDHABDD+HBJJ9F?A35DDIE?JJHIHJJIEE?JFJ?7JBGJJI>JJGJBJIIBIJJJIIIIJGJGJHHDFHF3FFFCB@,null]
479:[[chr1,72085323,72085423,chr1-11,TACTAGCCTTGAAAATGTTTAAAATAATATTCCAGAGTTAATATTGTTGTCCCTGGTATGTTAAAGAGTATTTGTTATCATAGCCAATTCTTGAGTCTGC,8@DDCD4D>D?C3DF(DCCHDDDA;HDEIBFCHGHHHFFIFEG1JHIJIJCGEJIHJG)IH(IJ)BDJ??FHHJHCJJIFJHJJJGIGH)2HFFFA=<CC,61G27A10,NM:i:2   AS:i:90 XS:i:0  RG:Z:foo,null]
480:[[chr1,214311329,214311429,chr1-10,GGTGATCCCTATTTGGTCCACTTTTGTTGGTAGTCTTCAAGCTTGATATCTGATTATCACTGTTGGAAGGTGTAAACTCACAGACTCAGAATTCTGGACT,D&++DDEDDC3+CB(@D8DDEHD;?FDF?DBI9A7@JFHJ(I(AIJJ@DHJIIJHII>HFG1JJFII<IJJJ(<HIJGHIJJE=FH@FHHHHFDDDFC@C,1A98,NM:i:1 AS:i:98 XS:i:0  RG:Z:foo,null]
481:[[chr1,152012628,152012728,chr1-9,AAGCAATTCTCTTGCTTTAGCCTCCCGAGAAGCTCGGATTACAGGCATGTCCACCACACCCAGCTAATTCTTTTGTATTTTTAGTAGACATGGGGTTTTG,BC:FFDFFHHHFHJ9HIJHIJJJFIGJCI=H/IHH@IGJIJIJIGJJJJEEIB'JJDJJIJDIGICHEFD@D3:0A/(BECDDDDCBE>BD8DDDDDC8C,null]
482:[[chr1,79478959,79479059,chr1-8,GGCAACACTTGAGAACACAAAGTGAGTTCTCACTTTGGGCGGTGGTTTCAGGCTTCAGGGTGGAGTTTTGTCAGGAACCCAACCTTTTCTGCCTAGAATT,@CCFDFDADHHAHFIH@ICJJHI5?JIJ)GCFEIJHG=II)HIGI9JJIJGHEJHFI8EIDG)GCI4FJF?I8HCDH;DD0&3CFDDDD@C4DCD6ADD>,81C18,null]
483:[[chr1,178190760,178190860,chr1-7,GTAGCCGGAATAAACAGTCACTGTGAGTTGTCCATTTTAGAGCATAGGTTTTCAGGTGGTGAAGACCTGTCCTTAGTTGAATTTGTATGTGAATTAAACT,B?<;FDDFHHHHHJEGJFCJJIFJJJA=JHHGIIGJJIIGIGJ(D:DAFG7)&DJID9J)FCD/HHJEDFIJ<FJAF@D@DDADF?C@A@ADCDD@CDDD,52T47,null]
484:[[chr1,42572410,42572510,chr1-6,AACCCTTTATCAGGTATGTATTATAAACATCGACTCTGTGGCTTGCATTTTCATTCTCCTTATATATCTTTTGATGAATCAAAGTTTTTAATTTGAATAT,BCCFFFFDAH)HHJJHIGG,HFH2JIJJ4IDI93IJJ<=JJ>IH7IJIJBIBG)CFH7DHHFAHFHEDIFBEFH;EBICA?3DD5D(DDBACDC(BADD:,94T5,NM:i:1   AS:i:95 XS:i:19 RG:Z:foo,null]
485:[[chr1,153186634,153186734,46,chr1-5,GTCTTGACTCTTTATCCACTTTGCCAGTCTGTGTCTTGTAATTGGGGCATTTAGCCTATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCT,C1@?FF=FHHHHHI?JJEJFIIIHG:.?>EEJEI(JG9J'IIHIJIHIJGJGJFJ9FJAG4EEC:DADE8DAEJFCCBBCDAEDDDD-DDDD@+DBC8D+,NM:i:0  AS:i:100    XS:i:82 RG:Z:foo,null]
486:[[chr1,50361545,50361645,AGGATCAAATTCACACATAACAATATTAACCTTAAATGTAAATAGGCTAAATGCCCCAATTACAAGACACAGACTGGCAAAGTGGATAAAGAGTCAAGAC,+D8CBD+@DDDD-DDDDEADCBBCCFJEAD8EDAD:CEE4GAJF9JFJGJGJIHIJIHII'J9GJ(IEJEE>?.:GHIIIFJEJJ?IHHHHHF=FF?@1C,62A18T1A13A2,NM:i:4 AS:i:82 RG:Z:foo,null]
487:[[chr1,121241806,121241906,chr1-4,AAATGGAGCCTTGAACCAAATAAATAGGTAGTAAAGGTAAATTTAAAATATGAAAAAAAATTTTTTTGAAAGGCATATGTTGACGAGTATTATTTCCACT,CCDD<BDHCC:2DE>DDH3BDE(?5ED=GC(GBCJ>JDJDIAJ>DBGDFEDFIFIJJC?80IJ?GIFIIJIIJJJ+JC92JJJJIIJHDHFHDDFFFC:C,NM:i:0    AS:i:100    XS:i:100    RG:Z:foo,null]
488:[[chr1,145038404,145038504,AGTGGAAATAATACTCGTCAACATATGCCTTTCAAAAAAATTTTTTTTCATATTTTAAATTTACCTTTACTACCTATTTATTTGGTTCAAGGCTCCATTT,C:CFFFDDHFHDHJIIJJJJ29CJ+JJJIIJIIFIG?JI08?CJJIFIFDEFDGBD>JAIDJDJ>JCBG(CG=DE5?(EDB3HDD>ED2:CCHDB<DDCC,null]
489:[[chr1,206260325,206260427,74M2D26M,74^AT26,NM:i:2    AS:i:92 RG:Z:foo,null]
490:[[chr1,84685020,84685120,chr1-3,TATTATTAAAACTATAAATGGACCAATTAAACAAACGTGTCATGAGCCAAGGAATATAAACTAATTCTTTACACCTGAAGTCCTTTAAAATGATTTAATT,CCCDFFB=HHHFHJIIJ:E@J>JA2C<IEI2DGJHJGI8FJJIJJAHJCIJJJJ*JJ;F?HFDJCIJFDJ'CHECDEFD,DDFBCH<A7DCD-DDBDD(E,92C5A1,NM:i:2 AS:i:93 XS:i:19 RG:Z:foo,null]
491:[[chr1,62477841,62477941,chr1-2,TAGGAAAATGGAGAAACTTTAATATGAAATCTTCCTGTTTTTCACATTATGTTTAGATTGTTACAGCATAAAATTTCAGAAACATTGCAAAAAGTTTTAA,@C=FFDFDHHHH>GJ@IEJGJIIJJJJF@JHHIIGGJ<IHJIG/J*?GD>ICIAJFJIH)H7E?GHEDI>HHFAHC@)(D>DDDED<DCDD=DBBC5DDE,77C0A21,null]
492:[[chr1,11355149,11355249,chr1-1,ATTTATTGGCTGTCTTTCAGGCACATTTTAGCTGTCATCCAACATTCTCAACCTTAGTCCCCTTCTCTGGGCTAAGGGGAGAATGATGGTCCTACCCCAG,BC?DFFFFHH<FFJG(ICJIGJJIJJGIFJIJGJ(7FJJJJJFDHID)JCH=3DIJ5JGDI8@@I@A=>3<:IDCA9DDFFI(FADEBDCDCCDDB(DC>,NM:i:0    AS:i:100    XS:i:0  RG:Z:foo,null]
2016-06-03 14:15:39 WARN  ParquetRecordReader:193 - Can not initialize counter due to context is not a instance of TaskInputOutputContext,but is org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl
distinct:492
end

Process finished with exit code 0

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