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opencb / opencga

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is maintained and develop by its parent company Zetta Genomics. Please contact support@zettagenomics.com for bug report and feature requests.
Apache License 2.0
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Variant file remove fails even after successfully running the MapReduce job #1187

Open wbari opened 5 years ago

wbari commented 5 years ago

Remove variant file after loading fails even though MR runs successfully

opencga@a4cbf37fded8:/opt/opencga/bin$ ./opencga-analysis.sh variant remove --file ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -s test 2019-02-21 16:08:09 [main] WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-02-21 16:08:09 [main] INFO RecoverableZooKeeper:120 - Process identifier=hconnection-0x1b58ff9e connecting to ZooKeeper ensemble=zk0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk2-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:zookeeper.version=3.4.6-1569965, built on 02/20/2014 09:09 GMT 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:host.name=a4cbf37fded8 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.version=1.8.0_201 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.vendor=Oracle Corporation 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.home=/usr/lib/jvm/java-8-oracle/jre 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.class.path=:/opt/opencga/conf/hadoop/:/opt/opencga/libs/opencga-catalog-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/biodata-models-1.4.3-20190215.140004-29.jar:/opt/opencga/libs/ga4gh-0.6.0a5.jar:/opt/opencga/libs/htsjdk-2.16.0.jar:/opt/opencga/libs/commons-jexl-2.1.1.jar:/opt/opencga/libs/ngs-java-2.9.0.jar:/opt/opencga/libs/biodata-tools-1.4.3-20190215.140034-29.jar:/opt/opencga/libs/log4j-1.2.15.jar:/opt/opencga/libs/BigWig-1.0.jar:/opt/opencga/libs/sqlite-jdbc-3.15.1.jar:/opt/opencga/libs/rocksdbjni-4.5.1.jar:/opt/opencga/libs/biojava-alignment-4.1.0.jar:/opt/opencga/libs/biojava-core-4.1.0.jar:/opt/opencga/libs/biojava-phylo-4.1.0.jar:/opt/opencga/libs/forester-1.005.jar:/opt/opencga/libs/log4j-api-2.2.jar:/opt/opencga/libs/log4j-core-2.2.jar:/opt/opencga/libs/jackson-dataformat-yaml-2.9.7.jar:/opt/opencga/libs/snakeyaml-1.23.jar:/opt/opencga/libs/jackson-dataformat-xml-2.9.7.jar:/opt/opencga/libs/woodstox-core-5.0.3.jar:/opt/opencga/libs/slf4j-api-1.7.21.jar:/opt/opencga/libs/slf4j-log4j12-1.7.21.jar:/opt/opencga/libs/mail-1.4.7.jar:/opt/opencga/libs/activation-1.1.jar:/opt/opencga/libs/commons-datastore-mongodb-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/commons-datastore-core-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/mongo-java-driver-3.7.1.jar:/opt/opencga/libs/commons-datastore-solr-3.7.3-20190118.140511-6.jar:/opt/opencga/libs/commons-lib-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/jcommander-1.64.jar:/opt/opencga/libs/jackson-databind-2.9.7.jar:/opt/opencga/libs/avro-1.7.7.jar:/opt/opencga/libs/paranamer-2.3.jar:/opt/opencga/libs/snappy-java-1.0.5.jar:/opt/opencga/libs/commons-lang3-3.8.1.jar:/opt/opencga/libs/ant-1.8.2.jar:/opt/opencga/libs/ant-launcher-1.8.2.jar:/opt/opencga/libs/jersey-container-servlet-2.25.1.jar:/opt/opencga/libs/jetty-server-9.3.14.v20161028.jar:/opt/opencga/libs/javax.servlet-api-3.1.0.jar:/opt/opencga/libs/jetty-http-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-util-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-io-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-webapp-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-xml-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-servlet-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-security-9.3.14.v20161028.jar:/opt/opencga/libs/jjwt-0.7.0.jar:/opt/opencga/libs/adal4j-1.6.3.jar:/opt/opencga/libs/oauth2-oidc-sdk-5.64.4.jar:/opt/opencga/libs/javax.mail-1.6.1.jar:/opt/opencga/libs/jcip-annotations-1.0-1.jar:/opt/opencga/libs/json-smart-2.3.jar:/opt/opencga/libs/accessors-smart-1.2.jar:/opt/opencga/libs/asm-5.0.4.jar:/opt/opencga/libs/lang-tag-1.4.4.jar:/opt/opencga/libs/nimbus-jose-jwt-7.0.jar:/opt/opencga/libs/gson-2.8.0.jar:/opt/opencga/libs/commons-codec-1.11.jar:/opt/opencga/libs/azure-1.13.0.jar:/opt/opencga/libs/azure-client-authentication-1.5.4.jar:/opt/opencga/libs/azure-annotations-1.2.0.jar:/opt/opencga/libs/azure-mgmt-resources-1.13.0.jar:/opt/opencga/libs/rxjava-1.2.4.jar:/opt/opencga/libs/azure-mgmt-storage-1.13.0.jar:/opt/opencga/libs/azure-mgmt-network-1.13.0.jar:/opt/opencga/libs/azure-mgmt-compute-1.13.0.jar:/opt/opencga/libs/azure-mgmt-graph-rbac-1.13.0.jar:/opt/opencga/libs/azure-mgmt-keyvault-1.13.0.jar:/opt/opencga/libs/azure-keyvault-1.0.0.jar:/opt/opencga/libs/azure-keyvault-webkey-1.0.0.jar:/opt/opencga/libs/azure-mgmt-batch-1.13.0.jar:/opt/opencga/libs/azure-mgmt-trafficmanager-1.13.0.jar:/opt/opencga/libs/azure-mgmt-dns-1.13.0.jar:/opt/opencga/libs/azure-mgmt-redis-1.13.0.jar:/opt/opencga/libs/azure-mgmt-appservice-1.13.0.jar:/opt/opencga/libs/azure-mgmt-locks-1.13.0.jar:/opt/opencga/libs/azure-mgmt-eventhub-1.13.0.jar:/opt/opencga/libs/azure-mgmt-cdn-1.13.0.jar:/opt/opencga/libs/azure-mgmt-sql-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerinstance-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerregistry-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerservice-1.13.0.jar:/opt/opencga/libs/azure-mgmt-cosmosdb-1.13.0.jar:/opt/opencga/libs/azure-mgmt-search-1.13.0.jar:/opt/opencga/libs/azure-mgmt-msi-1.13.0.jar:/opt/opencga/libs/azure-mgmt-monitor-1.13.0.jar:/opt/opencga/libs/azure-mgmt-servicebus-1.13.0.jar:/opt/opencga/libs/joda-time-2.1.jar:/opt/opencga/libs/azure-mgmt-batchai-1.13.0.jar:/opt/opencga/libs/solr-solrj-6.4.2.jar:/opt/opencga/libs/commons-io-2.5.jar:/opt/opencga/libs/httpcore-4.4.1.jar:/opt/opencga/libs/httpmime-4.4.1.jar:/opt/opencga/libs/zookeeper-3.4.6.jar:/opt/opencga/libs/stax2-api-3.1.4.jar:/opt/opencga/libs/woodstox-core-asl-4.4.1.jar:/opt/opencga/libs/noggit-0.6.jar:/opt/opencga/libs/jcl-over-slf4j-1.7.7.jar:/opt/opencga/libs/azure-batch-4.0.1.jar:/opt/opencga/libs/azure-client-runtime-1.6.4.jar:/opt/opencga/libs/client-runtime-1.6.4.jar:/opt/opencga/libs/retrofit-2.4.0.jar:/opt/opencga/libs/okhttp-3.11.0.jar:/opt/opencga/libs/logging-interceptor-3.11.0.jar:/opt/opencga/libs/okhttp-urlconnection-3.11.0.jar:/opt/opencga/libs/converter-jackson-2.4.0.jar:/opt/opencga/libs/jackson-datatype-joda-2.9.4.jar:/opt/opencga/libs/adapter-rxjava-2.4.0.jar:/opt/opencga/libs/opencga-analysis-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/hpg-bigdata-analysis-1.0.0-beta4.jar:/opt/opencga/libs/hpg-bigdata-core-1.0.0-beta4.jar:/opt/opencga/libs/bionetdb-core-0.2.0-20190131.171519-2.jar:/opt/opencga/libs/biodata-formats-1.4.3-20190215.140020-29.jar:/opt/opencga/libs/neo4j-java-driver-1.4.5.jar:/opt/opencga/libs/paxtools-core-4.3.1.jar:/opt/opencga/libs/collections-generic-4.01.jar:/opt/opencga/libs/commons-math3-3.5.jar:/opt/opencga/libs/reflections-0.9.10.jar:/opt/opencga/libs/javassist-3.19.0-GA.jar:/opt/opencga/libs/annotations-2.0.1.jar:/opt/opencga/libs/opencga-storage-app-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-server-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-mongodb-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-client-1.4.0-rc3-dev.jar:/opt/opencga/libs/jersey-client-2.25.1.jar:/opt/opencga/libs/hk2-api-2.5.0-b32.jar:/opt/opencga/libs/hk2-utils-2.5.0-b32.jar:/opt/opencga/libs/aopalliance-repackaged-2.5.0-b32.jar:/opt/opencga/libs/hk2-locator-2.5.0-b32.jar:/opt/opencga/libs/jersey-media-multipart-2.25.1.jar:/opt/opencga/libs/mimepull-1.9.6.jar:/opt/opencga/libs/protobuf-java-3.5.1.jar:/opt/opencga/libs/grpc-all-1.9.1.jar:/opt/opencga/libs/grpc-auth-1.9.1.jar:/opt/opencga/libs/google-auth-library-credentials-0.9.0.jar:/opt/opencga/libs/grpc-core-1.9.1.jar:/opt/opencga/libs/error_prone_annotations-2.1.2.jar:/opt/opencga/libs/jsr305-3.0.0.jar:/opt/opencga/libs/instrumentation-api-0.4.3.jar:/opt/opencga/libs/opencensus-api-0.10.0.jar:/opt/opencga/libs/opencensus-contrib-grpc-metrics-0.10.0.jar:/opt/opencga/libs/grpc-context-1.9.1.jar:/opt/opencga/libs/grpc-netty-1.9.1.jar:/opt/opencga/libs/netty-codec-http2-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-http-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-4.1.17.Final.jar:/opt/opencga/libs/netty-handler-4.1.17.Final.jar:/opt/opencga/libs/netty-buffer-4.1.17.Final.jar:/opt/opencga/libs/netty-common-4.1.17.Final.jar:/opt/opencga/libs/netty-handler-proxy-4.1.17.Final.jar:/opt/opencga/libs/netty-transport-4.1.17.Final.jar:/opt/opencga/libs/netty-resolver-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-socks-4.1.17.Final.jar:/opt/opencga/libs/grpc-okhttp-1.9.1.jar:/opt/opencga/libs/okhttp-2.5.0.jar:/opt/opencga/libs/okio-1.13.0.jar:/opt/opencga/libs/grpc-protobuf-1.9.1.jar:/opt/opencga/libs/protobuf-java-util-3.5.1.jar:/opt/opencga/libs/proto-google-common-protos-1.0.0.jar:/opt/opencga/libs/grpc-protobuf-lite-1.9.1.jar:/opt/opencga/libs/grpc-protobuf-nano-1.9.1.jar:/opt/opencga/libs/protobuf-javanano-3.0.0-alpha-5.jar:/opt/opencga/libs/grpc-stub-1.9.1.jar:/opt/opencga/libs/grpc-testing-1.9.1.jar:/opt/opencga/libs/opencga-server-1.4.0-rc3-dev.jar:/opt/opencga/libs/jersey-media-json-jackson-2.25.1.jar:/opt/opencga/libs/jersey-entity-filtering-2.25.1.jar:/opt/opencga/libs/jackson-jaxrs-base-2.9.7.jar:/opt/opencga/libs/jackson-core-2.9.7.jar:/opt/opencga/libs/jackson-jaxrs-json-provider-2.9.7.jar:/opt/opencga/libs/jackson-module-jaxb-annotations-2.9.7.jar:/opt/opencga/libs/swagger-jersey2-jaxrs-1.5.21.jar:/opt/opencga/libs/swagger-jaxrs-1.5.21.jar:/opt/opencga/libs/swagger-core-1.5.21.jar:/opt/opencga/libs/swagger-models-1.5.21.jar:/opt/opencga/libs/swagger-annotations-1.5.21.jar:/opt/opencga/libs/jersey-container-servlet-core-2.25.1.jar:/opt/opencga/libs/javax.inject-2.5.0-b32.jar:/opt/opencga/libs/jersey-common-2.25.1.jar:/opt/opencga/libs/javax.annotation-api-1.2.jar:/opt/opencga/libs/jersey-guava-2.25.1.jar:/opt/opencga/libs/osgi-resource-locator-1.0.1.jar:/opt/opencga/libs/jersey-server-2.25.1.jar:/opt/opencga/libs/jersey-media-jaxb-2.25.1.jar:/opt/opencga/libs/validation-api-1.1.0.Final.jar:/opt/opencga/libs/javax.ws.rs-api-2.0.1.jar:/opt/opencga/libs/cellbase-client-4.6.2-20190109.100231-2.jar:/opt/opencga/libs/cellbase-core-4.6.2-SNAPSHOT.jar:/opt/opencga/libs/cellbase-lib-4.6.2-SNAPSHOT.jar:/opt/opencga/libs/redisson-2.2.0.jar:/opt/opencga/libs/reactor-stream-2.0.7.RELEASE.jar:/opt/opencga/libs/reactor-core-2.0.7.RELEASE.jar:/opt/opencga/libs/reactive-streams-1.0.0.jar:/opt/opencga/libs/jackson-dataformat-cbor-2.6.3.jar:/opt/opencga/libs/kryo-2.23.0.jar:/opt/opencga/libs/minlog-1.2.jar:/opt/opencga/libs/objenesis-2.1.jar:/opt/opencga/libs/httpclient-4.3.4.jar:/opt/opencga/libs/commons-logging-1.1.3.jar:/opt/opencga/libs/jackson-annotations-2.9.7.jar:/opt/opencga/libs/hamcrest-core-1.3.jar:/opt/opencga/libs/opencga-storage-hadoop-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/guava-19.0.jar:/opt/opencga/libs/opencga-storage-hadoop-deps-1.4.0-rc3-dev-hdp-2.6.5-shaded.jar:/opt/opencga/libs/htrace-core-3.1.0-incubating.jar:/opt/opencga/libs/commons-cli-1.2.jar:/opt/opencga/libs/avro-ipc-1.7.7.jar:/opt/opencga/libs/netty-3.4.0.Final.jar:/opt/opencga/libs/velocity-1.7.jar:/opt/opencga/libs/avro-mapred-1.7.7-hadoop2.jar:/opt/opencga/libs/avro-ipc-1.7.7-tests.jar:/opt/opencga/libs/commons-configuration-1.6.jar:/opt/opencga/libs/commons-digester-1.8.jar:/opt/opencga/libs/commons-beanutils-1.7.0.jar:/opt/opencga/libs/commons-beanutils-core-1.8.0.jar:/opt/opencga/libs/commons-lang-2.6.jar:/opt/opencga/libs/commons-net-3.1.jar:/opt/opencga/libs/commons-httpclient-3.1.jar:/opt/opencga/libs/curator-recipes-2.7.1.jar:/opt/opencga/libs/curator-client-2.7.1.jar:/opt/opencga/libs/curator-framework-2.7.1.jar:/opt/opencga/libs/leveldbjni-all-1.8.jar:/opt/opencga/libs/apacheds-kerberos-codec-2.0.0-M15.jar:/opt/opencga/libs/apacheds-i18n-2.0.0-M15.jar:/opt/opencga/libs/api-asn1-api-1.0.0-M20.jar:/opt/opencga/libs/api-util-1.0.0-M20.jar:/opt/opencga/libs/azure-storage-2.0.0.jar:/opt/opencga/libs/jetty-util-6.1.26.jar:/opt/opencga/libs/disruptor-3.3.0.jar:/opt/opencga/libs/metrics-core-2.2.0.jar:/opt/opencga/libs/commons-math-2.2.jar:/opt/opencga/libs/commons-compress-1.4.1.jar:/opt/opencga/libs/xz-1.0.jar:/opt/opencga/libs/netty-all-4.0.23.Final.jar:/opt/opencga/libs/jamon-runtime-2.4.1.jar:/opt/opencga/libs/jackson-core-asl-1.9.13.jar:/opt/opencga/libs/jackson-mapper-asl-1.9.13.jar:/opt/opencga/libs/jackson-jaxrs-1.9.13.jar:/opt/opencga/libs/jackson-xc-1.9.13.jar:/opt/opencga/libs/antlr-runtime-3.5.2.jar:/opt/opencga/libs/jline-2.11.jar:/opt/opencga/libs/sqlline-1.1.9.jar:/opt/opencga/libs/tephra-api-0.7.0.jar:/opt/opencga/libs/tephra-core-0.7.0.jar:/opt/opencga/libs/guice-3.0.jar:/opt/opencga/libs/javax.inject-1.jar:/opt/opencga/libs/aopalliance-1.0.jar:/opt/opencga/libs/guice-assistedinject-3.0.jar:/opt/opencga/libs/libthrift-0.9.0.jar:/opt/opencga/libs/fastutil-6.5.6.jar:/opt/opencga/libs/twill-common-0.6.0-incubating.jar:/opt/opencga/libs/twill-core-0.6.0-incubating.jar:/opt/opencga/libs/twill-api-0.6.0-incubating.jar:/opt/opencga/libs/asm-all-5.0.2.jar:/opt/opencga/libs/twill-discovery-api-0.6.0-incubating.jar:/opt/opencga/libs/twill-discovery-core-0.6.0-incubating.jar:/opt/opencga/libs/twill-zookeeper-0.6.0-incubating.jar:/opt/opencga/libs/metrics-core-3.1.0.jar:/opt/opencga/libs/tephra-hbase-compat-1.1-0.7.0.jar:/opt/opencga/libs/snappy-0.3.jar:/opt/opencga/libs/commons-collections-3.2.1.jar:/opt/opencga/libs/commons-csv-1.0.jar:/opt/opencga/libs/parquet-avro-1.7.0.jar:/opt/opencga/libs/parquet-column-1.7.0.jar:/opt/opencga/libs/parquet-common-1.7.0.jar:/opt/opencga/libs/parquet-encoding-1.7.0.jar:/opt/opencga/libs/parquet-generator-1.7.0.jar:/opt/opencga/libs/parquet-hadoop-1.7.0.jar:/opt/opencga/libs/parquet-jackson-1.7.0.jar:/opt/opencga/libs/parquet-format-2.3.0-incubating.jar:/opt/opencga/libs/opencga-app-1.4.0-rc3-dev.jar 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.io.tmpdir=/tmp 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:java.compiler= 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:os.name=Linux 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:os.arch=amd64 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:os.version=4.18.0-1011-azure 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:user.name=opencga 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:user.home=/home/opencga 2019-02-21 16:08:09 [main] INFO ZooKeeper:100 - Client environment:user.dir=/opt/opencga/bin 2019-02-21 16:08:09 [main] INFO ZooKeeper:438 - Initiating client connection, connectString=zk0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk2-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181 sessionTimeout=120000 watcher=org.apache.hadoop.hbase.zookeeper.PendingWatcher@702ed190 2019-02-21 16:08:09 [main-SendThread(10.0.0.9:2181)] INFO ClientCnxn:975 - Opening socket connection to server 10.0.0.9/10.0.0.9:2181. Will not attempt to authenticate using SASL (unknown error) 2019-02-21 16:08:09 [main-SendThread(10.0.0.9:2181)] INFO ClientCnxn:852 - Socket connection established to 10.0.0.9/10.0.0.9:2181, initiating session 2019-02-21 16:08:09 [main-SendThread(10.0.0.9:2181)] INFO ClientCnxn:1235 - Session establishment complete on server 10.0.0.9/10.0.0.9:2181, sessionid = 0x2690fc6e6b90c8f, negotiated timeout = 120000 2019-02-21 16:08:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:10 [main] WARN DynamicClassLoader:120 - Failed to identify the fs of dir /hbase/lib, ignored Cannot run program "/usr/lib/hdinsight-common/scripts/decrypt.sh": error=2, No such file or directory at org.apache.hadoop.fs.azurebfs.services.ShellDecryptionKeyProvider.getStorageAccountKey(ShellDecryptionKeyProvider.java:65) at org.apache.hadoop.fs.azurebfs.AbfsConfiguration.getStorageAccountKey(AbfsConfiguration.java:355) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystemStore.initializeClient(AzureBlobFileSystemStore.java:880) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystemStore.(AzureBlobFileSystemStore.java:181) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystem.initialize(AzureBlobFileSystem.java:108) at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2796) at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:99) at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2830) at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2812) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:390) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:179) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:374) at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295) at org.apache.hadoop.hbase.util.DynamicClassLoader.initTempDir(DynamicClassLoader.java:118) at org.apache.hadoop.hbase.util.DynamicClassLoader.(DynamicClassLoader.java:98) at org.apache.hadoop.hbase.protobuf.ProtobufUtil.(ProtobufUtil.java:251) at org.apache.hadoop.hbase.ClusterId.parseFrom(ClusterId.java:64) at org.apache.hadoop.hbase.zookeeper.ZKClusterId.readClusterIdZNode(ZKClusterId.java:75) at org.apache.hadoop.hbase.client.ZooKeeperRegistry.getClusterId(ZooKeeperRegistry.java:105) at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.retrieveClusterId(ConnectionManager.java:903) at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.(ConnectionManager.java:648) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:238) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:218) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:119) at org.opencb.opencga.storage.hadoop.utils.HBaseManager.getConnection(HBaseManager.java:124) at org.opencb.opencga.storage.hadoop.utils.HBaseManager.(HBaseManager.java:78) at org.opencb.opencga.storage.hadoop.variant.metadata.AbstractHBaseDBAdaptor.(AbstractHBaseDBAdaptor.java:48) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseProjectMetadataDBAdaptor.(HBaseProjectMetadataDBAdaptor.java:46) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:38) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:13) at org.opencb.opencga.storage.core.metadata.StudyConfigurationManager.(StudyConfigurationManager.java:77) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.getStudyConfigurationManager(HadoopVariantStorageEngine.java:922) at org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation.updateCatalogFromStudyConfiguration(StorageOperation.java:117) at org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:40) at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103) at org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98) at org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34) 2019-02-21 16:08:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:10 [main] INFO HBaseManager:128 - Opened Hadoop DB connection hconnection-0x1b58ff9e called from [java.lang.Thread.getStackTrace(Thread.java:1559), org.opencb.opencga.storage.hadoop.utils.HBaseManager.getConnection(HBaseManager.java:127), org.opencb.opencga.storage.hadoop.utils.HBaseManager.(HBaseManager.java:78), org.opencb.opencga.storage.hadoop.variant.metadata.AbstractHBaseDBAdaptor.(AbstractHBaseDBAdaptor.java:48), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseProjectMetadataDBAdaptor.(HBaseProjectMetadataDBAdaptor.java:46), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:38), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:13), org.opencb.opencga.storage.core.metadata.StudyConfigurationManager.(StudyConfigurationManager.java:77), org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.getStudyConfigurationManager(HadoopVariantStorageEngine.java:922), org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation.updateCatalogFromStudyConfiguration(StorageOperation.java:117), org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:40), org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241), org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264), org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103), org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98), org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34)] 2019-02-21 16:08:10 [main] INFO CatalogStudyConfigurationFactory:104 - Updating StudyConfiguration 1 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:11 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] INFO StudyConfigurationManager:1207 - Resuming last batch operation "remove" due to error. 2019-02-21 16:08:12 [main] INFO HBaseStudyConfigurationDBAdaptor:165 - Update StudyConfiguration test@GRCh37:test 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:12 [main] INFO HadoopVariantStorageEngine:653 - ------------------------------------------------------ 2019-02-21 16:08:12 [main] INFO HadoopVariantStorageEngine:654 - Remove files [1] in archive 'opencga_test_GRCh37_archive_1' and analysis table 'opencga_test_GRCh37_variants' 2019-02-21 16:08:12 [main] INFO HadoopVariantStorageEngine:655 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-2] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-2] INFO MRExecutor:79 - Delete from archive table 2019-02-21 16:08:12 [pool-1-thread-2] INFO MRExecutor:80 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:79 - Delete from variants table 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:80 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-3] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-3] INFO MRExecutor:79 - Delete from SamplesIndex table 2019-02-21 16:08:12 [pool-1-thread-3] INFO MRExecutor:80 - ------------------------------------------------------ 'hadoop' 'jar' '/home/sshuser/opencga//opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar' 'org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver' 'opencga_test_GRCh37_archive_1' 'columns_to_delete' '0:1_R,0:1_N' 'database.name' 'opencga' 'dbadaptor.phoenix.fetch_size' '-1' 'annotator' 'cellbase_rest' 'annotator.cellbase.exclude' 'expression' 'annotator.cellbase.use_cache' 'true' 'annotator.cellbase.imprecise_variants' 'false' 'opencga.storage.hadoop.jar-with-dependencies' 'opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar' 'opencga.archive.chunk_size' '1000' 'hadoop.load.archive.batch.size' '3' 'hadoop.load.variant.batch.size' '500' 'opencga.archive.table.presplit.size' '500' 'opencga.archive.table.compression' 'gz' 'opencga.variant.table.presplit.size' '500' 'opencga.variant.table.compression' 'snappy' 'opencga.sample-index.table.presplit.size' '15' 'opencga.sample-index.table.compression' 'snappy' 'intersect.active' 'true' 'intersect.always' 'false' 'intersect.params.threshold' '3' 'opencga.hadoop.bin' 'hadoop' 'opencga.mr.executor' 'ssh' 'mapreduce.map.cpu.vcores' '1' 'mapreduce.map.memory.mb' '2560' 'opencga.variant.table.mapreduce.map.java.opts' '-Xmx2048m,-XX:+UseG1GC,-Djava.util.concurrent.ForkJoinPool.common.parallelism=1' 'opencga.storage.hadoop.hbase.merge.archive.scan.batchsize' '2000' 'opencga.storage.hadoop.mapreduce.scanner.timeout' '300000' 'opencga.mr.executor.ssh.host' 'cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net' 'opencga.mr.executor.ssh.user' 'sshuser' 'opencga.mr.executor.ssh.password' 'f1d5971-d266-4113-adf1-212aeb6409bH' 'opencga.mr.executor.ssh.remote_opencga_home' '/home/sshuser/opencga/' 'resume' 'false' 'opencga.variant.table.timestamp' '1550759141753' 'delete.hbase.column.mapper.class' 'org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine$MyDeleteHBaseColumnMapper' Connect to Hadoop edge node sshuser@cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net sshpass -e ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60 sshuser@cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net Connect to Hadoop edge node sshuser@cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net sshpass -e ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60 sshuser@cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net 'hadoop' 'jar' '/home/sshuser/opencga//opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar' 'org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver' 'opencga_test_GRCh37_variants' 'columns_to_delete' 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'database.name' 'opencga' 'dbadaptor.phoenix.fetch_size' '-1' 'annotator' 'cellbase_rest' 'annotator.cellbase.exclude' 'expression' 'annotator.cellbase.use_cache' 'true' 'annotator.cellbase.imprecise_variants' 'false' 'opencga.storage.hadoop.jar-with-dependencies' 'opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar' 'opencga.archive.chunk_size' '1000' 'hadoop.load.archive.batch.size' '3' 'hadoop.load.variant.batch.size' '500' 'opencga.archive.table.presplit.size' '500' 'opencga.archive.table.compression' 'gz' 'opencga.variant.table.presplit.size' '500' 'opencga.variant.table.compression' 'snappy' 'opencga.sample-index.table.presplit.size' '15' 'opencga.sample-index.table.compression' 'snappy' 'intersect.active' 'true' 'intersect.always' 'false' 'intersect.params.threshold' '3' 'opencga.hadoop.bin' 'hadoop' 'opencga.mr.executor' 'ssh' 'mapreduce.map.cpu.vcores' '1' 'mapreduce.map.memory.mb' '2560' 'opencga.variant.table.mapreduce.map.java.opts' '-Xmx2048m,-XX:+UseG1GC,-Djava.util.concurrent.ForkJoinPool.common.parallelism=1' 'opencga.storage.hadoop.hbase.merge.archive.scan.batchsize' '2000' 'opencga.storage.hadoop.mapreduce.scanner.timeout' '300000' 'opencga.mr.executor.ssh.host' 'cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net' 'opencga.mr.executor.ssh.user' 'sshuser' 'opencga.mr.executor.ssh.password' 'f1d5971-d266-4113-adf1-212aeb6409bH' 'opencga.mr.executor.ssh.remote_opencga_home' '/home/sshuser/opencga/' 'resume' 'false' 'opencga.variant.table.timestamp' '1550759141753' 'delete.hbase.column.mapper.class' 'org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine$MyDeleteHBaseColumnMapper' ssh_exchange_identification: read: Connection reset by peer 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:82 - ------------------------------------------------------ 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:83 - Exit value: 255 2019-02-21 16:08:12 [pool-1-thread-1] INFO MRExecutor:84 - Total time: 0.166s Warning: Permanently added 'cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net,40.85.134.222' (ECDSA) to the list of known hosts. Authorized uses only. All activity may be monitored and reported. 2019-02-21 16:08:29,533 INFO [main] utils.AbstractHBaseDriver: [opencga_test_GRCh37_archive_1, columns_to_delete, 0:1_R,0:1_N, database.name, opencga, dbadaptor.phoenix.fetch_size, -1, annotator, cellbase_rest, annotator.cellbase.exclude, expression, annotator.cellbase.use_cache, true, annotator.cellbase.imprecise_variants, false, opencga.storage.hadoop.jar-with-dependencies, opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar, opencga.archive.chunk_size, 1000, hadoop.load.archive.batch.size, 3, hadoop.load.variant.batch.size, 500, opencga.archive.table.presplit.size, 500, opencga.archive.table.compression, gz, opencga.variant.table.presplit.size, 500, opencga.variant.table.compression, snappy, opencga.sample-index.table.presplit.size, 15, opencga.sample-index.table.compression, snappy, intersect.active, true, intersect.always, false, intersect.params.threshold, 3, opencga.hadoop.bin, hadoop, opencga.mr.executor, ssh, mapreduce.map.cpu.vcores, 1, mapreduce.map.memory.mb, 2560, opencga.variant.table.mapreduce.map.java.opts, -Xmx2048m,-XX:+UseG1GC,-Djava.util.concurrent.ForkJoinPool.common.parallelism=1, opencga.storage.hadoop.hbase.merge.archive.scan.batchsize, 2000, opencga.storage.hadoop.mapreduce.scanner.timeout, 300000, opencga.mr.executor.ssh.host, cgahbasejruwjaf7pg2iw-ssh.azurehdinsight.net, opencga.mr.executor.ssh.user, sshuser, opencga.mr.executor.ssh.password, f1d5971-d266-4113-adf1-212aeb6409bH, opencga.mr.executor.ssh.remote_opencga_home, /home/sshuser/opencga/, resume, false, opencga.variant.table.timestamp, 1550759141753, delete.hbase.column.mapper.class, org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine$MyDeleteHBaseColumnMapper] 2019-02-21 16:08:29,799 INFO [main] utils.DeleteHBaseColumnDriver: Scan set Caching to 100 2019-02-21 16:08:29,806 INFO [main] mr.VariantMapReduceUtil: Use table opencga_test_GRCh37_archive_1 as input 2019-02-21 16:08:30,780 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:31,289 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:31,324 INFO [main] mr.VariantMapReduceUtil: Use table opencga_test_GRCh37_archive_1 as output 2019-02-21 16:08:31,369 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:31,371 INFO [main] Configuration.deprecation: io.bytes.per.checksum is deprecated. Instead, use dfs.bytes-per-checksum 2019-02-21 16:08:31,391 INFO [main] utils.AbstractHBaseDriver: ================================================= 2019-02-21 16:08:31,392 INFO [main] utils.AbstractHBaseDriver: Execute opencga: delete columns from table 'opencga_test_GRCh37_archive_1' 2019-02-21 16:08:31,392 INFO [main] utils.AbstractHBaseDriver: ================================================= 2019-02-21 16:08:31,485 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:31,739 INFO [main] client.AHSProxy: Connecting to Application History server at headnodehost/10.0.0.17:10200 2019-02-21 16:08:31,797 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:31,799 INFO [main] Configuration.deprecation: io.bytes.per.checksum is deprecated. Instead, use dfs.bytes-per-checksum 2019-02-21 16:08:31,971 INFO [main] client.RequestHedgingRMFailoverProxyProvider: Looking for the active RM in [rm1, rm2]... 2019-02-21 16:08:32,523 INFO [main] client.RequestHedgingRMFailoverProxyProvider: Found active RM [rm1] 2019-02-21 16:08:35,975 WARN [main] conf.Configuration: hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:08:36,013 INFO [main] zookeeper.RecoverableZooKeeper: Process identifier=hconnection-0x4bb7b1b1 connecting to ZooKeeper ensemble=zk0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk2-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181 2019-02-21 16:08:36,018 INFO [main] zookeeper.ZooKeeper: Client environment:zookeeper.version=3.4.6-3--1, built on 01/25/2019 18:17 GMT 2019-02-21 16:08:36,018 INFO [main] zookeeper.ZooKeeper: Client environment:host.name=hn0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net 2019-02-21 16:08:36,019 INFO [main] zookeeper.ZooKeeper: Client environment:java.version=1.8.0_191 2019-02-21 16:08:36,019 INFO [main] zookeeper.ZooKeeper: Client environment:java.vendor=Oracle Corporation 2019-02-21 16:08:36,020 INFO [main] zookeeper.ZooKeeper: Client environment:java.home=/usr/lib/jvm/java-8-openjdk-amd64/jre 2019-02-21 16:08:36,020 INFO [main] zookeeper.ZooKeeper: Client environment:java.class.path=/home/sshuser/opencga/libs/protobuf-java-3.5.1.jar:/home/sshuser/opencga/libs/protobuf-java-util-3.5.1.jar:/home/sshuser/opencga/libs/avro-ipc-1.7.7.jar:/home/sshuser/opencga/libs/avro-1.7.7.jar:/home/sshuser/opencga/libs/avro-ipc-1.7.7-tests.jar:/home/sshuser/opencga/libs/avro-mapred-1.7.7-hadoop2.jar:/home/sshuser/opencga/libs/jackson-jaxrs-base-2.9.7.jar:/home/sshuser/opencga/libs/jackson-dataformat-yaml-2.9.7.jar:/home/sshuser/opencga/libs/jackson-module-jaxb-annotations-2.9.7.jar:/home/sshuser/opencga/libs/jackson-dataformat-cbor-2.6.3.jar:/home/sshuser/opencga/libs/jackson-core-2.9.7.jar:/home/sshuser/opencga/libs/jackson-jaxrs-json-provider-2.9.7.jar:/home/sshuser/opencga/libs/jackson-datatype-joda-2.9.4.jar:/home/sshuser/opencga/libs/jackson-databind-2.9.7.jar:/home/sshuser/opencga/libs/jackson-annotations-2.9.7.jar:/home/sshuser/opencga/libs/jackson-dataformat-xml-2.9.7.jar:/home/sshuser/opencga/conf/hadoop/:/usr/hdp/current/hadoop-mapreduce-client/hadoop-streaming-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-sls.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-jobclient.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-ant-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-rumen-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/activation-1.1.jar:/usr/hdp/current/hadoop-mapreduce-client/zookeeper-3.4.6.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-compress-1.4.1.jar:/usr/hdp/current/hadoop-mapreduce-client/api-util-1.0.0-M20.jar:/usr/hdp/current/hadoop-mapreduce-client/jaxb-api-2.2.2.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-gridmix-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-core.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-httpclient-3.1.jar:/usr/hdp/current/hadoop-mapreduce-client/servlet-api-2.5.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-ant.jar:/usr/hdp/current/hadoop-mapreduce-client/jackson-jaxrs-1.9.13.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-hs-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/curator-client-2.7.1.jar:/usr/hdp/current/hadoop-mapreduce-client/httpcore-4.4.4.jar:/usr/hdp/current/hadoop-mapreduce-client/apacheds-kerberos-codec-2.0.0-M15.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-configuration-1.6.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-collections-3.2.2.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-app-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/jettison-1.1.jar:/usr/hdp/current/hadoop-mapreduce-client/hamcrest-core-1.3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-distcp-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/jets3t-0.9.0.jar:/usr/hdp/current/hadoop-mapreduce-client/jackson-xc-1.9.13.jar:/usr/hdp/current/hadoop-mapreduce-client/protobuf-java-2.5.0.jar:/usr/hdp/current/hadoop-mapreduce-client/jetty-sslengine-6.1.26.hwx.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-auth.jar:/usr/hdp/current/hadoop-mapreduce-client/azure-keyvault-core-1.0.0.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-extras.jar:/usr/hdp/current/hadoop-mapreduce-client/jackson-mapper-asl-1.9.13.jar:/usr/hdp/current/hadoop-mapreduce-client/mockito-all-1.8.5.jar:/usr/hdp/current/hadoop-mapreduce-client/netty-3.6.2.Final.jar:/usr/hdp/current/hadoop-mapreduce-client/jcip-annotations-1.0-1.jar:/usr/hdp/current/hadoop-mapreduce-client/metrics-core-3.0.1.jar:/usr/hdp/current/hadoop-mapreduce-client/jersey-server-1.9.jar:/usr/hdp/current/hadoop-mapreduce-client/paranamer-2.3.jar:/usr/hdp/current/hadoop-mapreduce-client/xz-1.0.jar:/usr/hdp/current/hadoop-mapreduce-client/jackson-core-asl-1.9.13.jar:/usr/hdp/current/hadoop-mapreduce-client/nimbus-jose-jwt-4.41.1.jar:/usr/hdp/current/hadoop-mapreduce-client/avro-1.7.4.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-io-2.4.jar:/usr/hdp/current/hadoop-mapreduce-client/stax-api-1.0-2.jar:/usr/hdp/current/hadoop-mapreduce-client/snappy-java-1.0.4.1.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-beanutils-1.7.0.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-net-3.1.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-jobclient-2.7.3.2.6.5.3007-3-tests.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-core-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-cli-1.2.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-app.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-openstack.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-shuffle-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-math3-3.1.1.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-lang-2.6.jar:/usr/hdp/current/hadoop-mapreduce-client/java-xmlbuilder-0.4.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-openstack-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/jetty-6.1.26.hwx.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-examples.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-beanutils-core-1.8.0.jar:/usr/hdp/current/hadoop-mapreduce-client/json-smart-1.3.1.jar:/usr/hdp/current/hadoop-mapreduce-client/jetty-util-6.1.26.hwx.jar:/usr/hdp/current/hadoop-mapreduce-client/jaxb-impl-2.2.3-1.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-datajoin-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/api-asn1-api-1.0.0-M20.jar:/usr/hdp/current/hadoop-mapreduce-client/jersey-core-1.9.jar:/usr/hdp/current/hadoop-mapreduce-client/jsp-api-2.1.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-shuffle.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-lang3-3.4.jar:/usr/hdp/current/hadoop-mapreduce-client/asm-3.2.jar:/usr/hdp/current/hadoop-mapreduce-client/jsr305-3.0.0.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-hs-plugins-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-common.jar:/usr/hdp/current/hadoop-mapreduce-client/jsch-0.1.54.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-examples-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/xmlenc-0.52.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-archives-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-auth-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-logging-1.1.3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-streaming.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-distcp.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-hs.jar:/usr/hdp/current/hadoop-mapreduce-client/apacheds-i18n-2.0.0-M15.jar:/usr/hdp/current/hadoop-mapreduce-client/htrace-core-3.1.0-incubating.jar:/usr/hdp/current/hadoop-mapreduce-client/log4j-1.2.17.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-hs-plugins.jar:/usr/hdp/current/hadoop-mapreduce-client/curator-recipes-2.7.1.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-rumen.jar:/usr/hdp/current/hadoop-mapreduce-client/wildfly-openssl-1.0.4.Final.jar:/usr/hdp/current/hadoop-mapreduce-client/curator-framework-2.7.1.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-digester-1.8.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-datajoin.jar:/usr/hdp/current/hadoop-mapreduce-client/guava-11.0.2.jar:/usr/hdp/current/hadoop-mapreduce-client/junit-4.11.jar:/usr/hdp/current/hadoop-mapreduce-client/httpclient-4.5.2.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-extras-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-gridmix.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-jobclient-2.7.3.2.6.5.3007-3.jar:/usr/hdp/current/hadoop-mapreduce-client/gson-2.2.4.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-mapreduce-client-jobclient-tests.jar:/usr/hdp/current/hadoop-mapreduce-client/jersey-json-1.9.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-archives.jar:/usr/hdp/current/hadoop-mapreduce-client/commons-codec-1.4.jar:/usr/hdp/current/hadoop-mapreduce-client/hadoop-sls-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/conf:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-hadoop1-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-spi-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/activation-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/zookeeper-3.4.6.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-compress-1.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/api-util-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jaxb-api-2.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-hadoop2-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-bookkeeper-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/aws-java-sdk-core-1.10.6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/servlet-api-2.5.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-presto-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-jaxrs-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/curator-client-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-databind-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/httpcore-4.4.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-rpm-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/hadoop-lzo-0.6.0.2.6.5.3007-3-sources.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/slf4j-api-1.7.10.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/apacheds-kerberos-codec-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-configuration-1.6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-collections-3.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jettison-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/hamcrest-core-1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jets3t-0.9.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-xc-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jetty-sslengine-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/azure-keyvault-core-1.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/json-simple-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-mapper-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/mockito-all-1.8.5.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/netty-3.6.2.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jcip-annotations-1.0-1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jersey-server-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/paranamer-2.3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/xz-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-core-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/nimbus-jose-jwt-4.41.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/avro-1.7.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/ranger-hdfs-plugin-shim-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/stax-api-1.0-2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/snappy-java-1.0.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-beanutils-1.7.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-core-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-net-3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/aws-java-sdk-s3-1.10.6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/ojdbc6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/json-20090211.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-cli-1.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-math3-3.1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-core-0.3.0.2.6.99.201-SNAPSHOT-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-lang-2.6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/aws-java-sdk-kms-1.10.6.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/java-xmlbuilder-0.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jetty-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/hadoop-lzo-0.6.0.2.6.5.3007-3-javadoc.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-beanutils-core-1.8.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/json-smart-1.3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jetty-util-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-annotations-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jaxb-impl-2.2.3-1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-tests-0.3.0.2.6.99.201-SNAPSHOT.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/api-asn1-api-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/hadoop-lzo-0.6.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jersey-core-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jsp-api-2.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/ranger-yarn-plugin-shim-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/azure-storage-7.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jackson-core-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-lang3-3.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/asm-3.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/ranger-plugin-classloader-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jsr305-3.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/microsoft-log4j-etwappender-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jsch-0.1.54.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/xmlenc-0.52.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-logging-1.1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/joda-time-2.9.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/apacheds-i18n-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/htrace-core-3.1.0-incubating.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/log4j-1.2.17.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/rubix-tests-0.3.0.2.6.99.201-SNAPSHOT-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/curator-recipes-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/curator-framework-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-digester-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/guava-11.0.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/junit-4.11.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/slf4j-log4j12-1.7.10.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/mdsdclient-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/httpclient-4.5.2.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/gson-2.2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/jersey-json-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop/lib/commons-codec-1.4.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-aws-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-aws.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-annotations.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-auth.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-azure-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-annotations-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-nfs.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-azure.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-common-2.7.3.2.6.5.3007-3-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-nfs-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-common.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//azure-data-lake-store-sdk-2.2.5.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-common-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-auth-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-azure-datalake.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//hadoop-azure-datalake-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop/.//gcs-connector-1.8.1.2.6.5.3007-3-shaded.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/./:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/xml-apis-1.3.04.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/xercesImpl-2.9.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/netty-all-4.0.52.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/servlet-api-2.5.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jackson-databind-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/json-simple-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jackson-mapper-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/netty-3.6.2.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jersey-server-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jackson-core-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/json-20090211.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/adls2-oauth2-token-provider-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-cli-1.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-lang-2.6.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jetty-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/leveldbjni-all-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/adls2-oauth2-token-provider.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jetty-util-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jackson-annotations-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-daemon-1.0.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/azure-data-lake-store-sdk.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/okio-1.6.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jersey-core-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jackson-core-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/asm-3.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/jsr305-3.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/microsoft-log4j-etwappender-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/xmlenc-0.52.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-logging-1.1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/htrace-core-3.1.0-incubating.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/log4j-1.2.17.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/hadoop-azure-datalake.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/guava-11.0.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/mdsdclient-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/okhttp-2.7.5.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/lib/commons-codec-1.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs-2.7.3.2.6.5.3007-3-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs-nfs-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs-nfs.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-hdfs/.//hadoop-hdfs.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/activation-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/zookeeper-3.4.6.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-compress-1.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/api-util-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jaxb-api-2.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/mssql-jdbc-7.0.0.jre8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/servlet-api-2.5.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-jaxrs-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/objenesis-2.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/curator-client-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-databind-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/httpcore-4.4.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/apacheds-kerberos-codec-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-configuration-1.6.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-collections-3.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jettison-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jets3t-0.9.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-xc-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jetty-sslengine-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/aopalliance-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/azure-keyvault-core-1.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jersey-client-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/json-simple-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-mapper-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/netty-3.6.2.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jcip-annotations-1.0-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/metrics-core-3.0.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/zookeeper-3.4.6.2.6.5.3007-3-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jersey-server-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/paranamer-2.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/xz-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-core-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/nimbus-jose-jwt-4.41.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jersey-guice-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/avro-1.7.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/stax-api-1.0-2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/snappy-java-1.0.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-beanutils-1.7.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/guice-servlet-3.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-net-3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/guice-3.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/json-20090211.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-cli-1.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/hdinsight-ats-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-math3-3.1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/javassist-3.18.1-GA.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-lang-2.6.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/java-xmlbuilder-0.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/javax.inject-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jetty-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/leveldbjni-all-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-beanutils-core-1.8.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/json-smart-1.3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jetty-util-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-annotations-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-dbcp2-2.0.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jaxb-impl-2.2.3-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/api-asn1-api-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jersey-core-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jsp-api-2.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/azure-storage-7.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-pool2-2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jackson-core-2.7.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-lang3-3.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/asm-3.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jsr305-3.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/fst-2.24.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/microsoft-log4j-etwappender-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jsch-0.1.54.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/xmlenc-0.52.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-logging-1.1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/apacheds-i18n-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/htrace-core-3.1.0-incubating.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/log4j-1.2.17.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/curator-recipes-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/wildfly-openssl-1.0.4.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/curator-framework-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-digester-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/guava-11.0.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/mdsdclient-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/httpclient-4.5.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/gson-2.2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/jersey-json-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/lib/commons-codec-1.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-registry-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-timeline-pluginstorage-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-applicationhistoryservice-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-tests-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-common.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-resourcemanager.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-api.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-web-proxy.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-sharedcachemanager-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-applicationhistoryservice.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-web-proxy-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-client.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-applications-distributedshell.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-applications-unmanaged-am-launcher-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-nodemanager-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-api-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-applications-distributedshell-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-nodemanager.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-common.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-registry.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-sharedcachemanager.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-client-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-resourcemanager-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-applications-unmanaged-am-launcher.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-yarn/.//hadoop-yarn-server-timeline-pluginstorage.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/commons-compress-1.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/mssql-jdbc-7.0.0.jre8.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/hamcrest-core-1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/aopalliance-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/jackson-mapper-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/netty-3.6.2.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/jersey-server-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/paranamer-2.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/xz-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/jackson-core-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/jersey-guice-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/avro-1.7.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/snappy-java-1.0.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/guice-servlet-3.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/guice-3.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/hdinsight-ats-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/javax.inject-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/leveldbjni-all-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/commons-dbcp2-2.0.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/jersey-core-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/commons-pool2-2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/asm-3.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/log4j-1.2.17.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/lib/junit-4.11.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-streaming-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-sls.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-jobclient.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-ant-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-rumen-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//activation-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//zookeeper-3.4.6.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-compress-1.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//api-util-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jaxb-api-2.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-gridmix-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-core.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-httpclient-3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//servlet-api-2.5.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-ant.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jackson-jaxrs-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-hs-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//curator-client-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//httpcore-4.4.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//apacheds-kerberos-codec-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-configuration-1.6.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-collections-3.2.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-app-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jettison-1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hamcrest-core-1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-distcp-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jets3t-0.9.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jackson-xc-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jetty-sslengine-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-auth.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//azure-keyvault-core-1.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-extras.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jackson-mapper-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//mockito-all-1.8.5.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//netty-3.6.2.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jcip-annotations-1.0-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//metrics-core-3.0.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jersey-server-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//paranamer-2.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//xz-1.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jackson-core-asl-1.9.13.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//nimbus-jose-jwt-4.41.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//avro-1.7.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//stax-api-1.0-2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//snappy-java-1.0.4.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-beanutils-1.7.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-net-3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-jobclient-2.7.3.2.6.5.3007-3-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-core-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-cli-1.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-app.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-openstack.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-shuffle-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-math3-3.1.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-lang-2.6.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//java-xmlbuilder-0.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-openstack-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jetty-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-examples.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-beanutils-core-1.8.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//json-smart-1.3.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jetty-util-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jaxb-impl-2.2.3-1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-datajoin-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//api-asn1-api-1.0.0-M20.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jersey-core-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jsp-api-2.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-shuffle.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-lang3-3.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//asm-3.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jsr305-3.0.0.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-hs-plugins-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-common.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jsch-0.1.54.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-examples-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//xmlenc-0.52.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-archives-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-auth-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-logging-1.1.3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-streaming.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-distcp.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-hs.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//apacheds-i18n-2.0.0-M15.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//htrace-core-3.1.0-incubating.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//log4j-1.2.17.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-hs-plugins.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//curator-recipes-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-rumen.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//wildfly-openssl-1.0.4.Final.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//curator-framework-2.7.1.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-digester-1.8.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-datajoin.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//guava-11.0.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//junit-4.11.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//httpclient-4.5.2.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-extras-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-gridmix.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-jobclient-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//gson-2.2.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-mapreduce-client-jobclient-tests.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//jersey-json-1.9.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-archives.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//commons-codec-1.4.jar:/usr/hdp/2.6.5.3007-3/hadoop-mapreduce/.//hadoop-sls-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-examples-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-api-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-yarn-timeline-history-with-acls-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-tests-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-history-parser-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-yarn-timeline-cache-plugin-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-mapreduce-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-dag-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-yarn-timeline-history-with-fs-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-runtime-internals-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-job-analyzer-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-runtime-library-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-yarn-timeline-history-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/tez-common-0.7.0.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-collections4-4.1.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-yarn-server-timeline-pluginstorage-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/servlet-api-2.5.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-aws-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-collections-3.2.2.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jettison-1.3.4.jar:/usr/hdp/2.6.5.3007-3/tez/lib/protobuf-java-2.5.0.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-azure-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jersey-client-1.9.jar:/usr/hdp/2.6.5.3007-3/tez/lib/slf4j-api-1.7.5.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-annotations-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-io-2.4.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-yarn-server-web-proxy-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jsr305-2.0.3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/metrics-core-3.1.0.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-mapreduce-client-core-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-cli-1.2.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-math3-3.1.1.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-lang-2.6.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jetty-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jetty-util-6.1.26.hwx.jar:/usr/hdp/2.6.5.3007-3/tez/lib/azure-data-lake-store-sdk-2.1.4.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-mapreduce-client-common-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/hadoop-azure-datalake-2.7.3.2.6.5.3007-3.jar:/usr/hdp/2.6.5.3007-3/tez/lib/gcs-connector-1.8.1.2.6.5.3007-3-shaded.jar:/usr/hdp/2.6.5.3007-3/tez/lib/guava-11.0.2.jar:/usr/hdp/2.6.5.3007-3/tez/lib/jersey-json-1.9.jar:/usr/hdp/2.6.5.3007-3/tez/lib/commons-codec-1.4.jar:/usr/hdp/2.6.5.3007-3/tez/conf 2019-02-21 16:08:36,024 INFO [main] zookeeper.ZooKeeper: Client environment:java.library.path=:/usr/hdp/2.6.5.3007-3/hadoop/lib/native/Linux-amd64-64:/usr/lib/hadoop/lib/native/Linux-amd64-64:/usr/hdp/2.6.5.3007-3/hadoop/lib/native 2019-02-21 16:08:36,024 INFO [main] zookeeper.ZooKeeper: Client environment:java.io.tmpdir=/tmp 2019-02-21 16:08:36,024 INFO [main] zookeeper.ZooKeeper: Client environment:java.compiler= 2019-02-21 16:08:36,025 INFO [main] zookeeper.ZooKeeper: Client environment:os.name=Linux 2019-02-21 16:08:36,025 INFO [main] zookeeper.ZooKeeper: Client environment:os.arch=amd64 2019-02-21 16:08:36,026 INFO [main] zookeeper.ZooKeeper: Client environment:os.version=4.15.0-1037-azure 2019-02-21 16:08:36,026 INFO [main] zookeeper.ZooKeeper: Client environment:user.name=sshuser 2019-02-21 16:08:36,027 INFO [main] zookeeper.ZooKeeper: Client environment:user.home=/home/sshuser 2019-02-21 16:08:36,027 INFO [main] zookeeper.ZooKeeper: Client environment:user.dir=/home/sshuser 2019-02-21 16:08:36,028 INFO [main] zookeeper.ZooKeeper: Initiating client connection, connectString=zk0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181,zk2-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181 sessionTimeout=120000 watcher=org.apache.hadoop.hbase.zookeeper.PendingWatcher@66240806 2019-02-21 16:08:36,049 INFO [main-SendThread(zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181)] zookeeper.ClientCnxn: Opening socket connection to server zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net/10.0.0.14:2181. Will not attempt to authenticate using SASL (unknown error) 2019-02-21 16:08:36,051 INFO [main-SendThread(zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181)] zookeeper.ClientCnxn: Socket connection established, initiating session, client: /10.0.0.18:40442, server: zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net/10.0.0.14:2181 2019-02-21 16:08:36,081 INFO [main-SendThread(zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:2181)] zookeeper.ClientCnxn: Session establishment complete on server zk4-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net/10.0.0.14:2181, sessionid = 0x3690fc6e7480ce6, negotiated timeout = 120000 2019-02-21 16:08:36,165 INFO [main] util.RegionSizeCalculator: Calculating region sizes for table "opencga_test_GRCh37_archive_1". 2019-02-21 16:08:40,357 INFO [main] client.ConnectionManager$HConnectionImplementation: Closing master protocol: MasterService 2019-02-21 16:08:40,361 INFO [main] client.ConnectionManager$HConnectionImplementation: Closing zookeeper sessionid=0x3690fc6e7480ce6 2019-02-21 16:08:40,382 INFO [main] zookeeper.ZooKeeper: Session: 0x3690fc6e7480ce6 closed 2019-02-21 16:08:40,382 INFO [main-EventThread] zookeeper.ClientCnxn: EventThread shut down 2019-02-21 16:08:40,545 INFO [main] mapreduce.JobSubmitter: number of splits:3001 2019-02-21 16:08:40,611 INFO [main] Configuration.deprecation: io.bytes.per.checksum is deprecated. Instead, use dfs.bytes-per-checksum 2019-02-21 16:08:40,696 INFO [main] mapreduce.JobSubmitter: Submitting tokens for job: job_1550764007219_0001 2019-02-21 16:08:41,181 INFO [main] impl.YarnClientImpl: Submitted application application_1550764007219_0001 2019-02-21 16:08:41,211 INFO [main] mapreduce.Job: The url to track the job: http://hn0-cgahba.mrjrzbp2r4le5alqz1hxmd2ace.fx.internal.cloudapp.net:8088/proxy/application_1550764007219_0001/ 2019-02-21 16:08:41,212 INFO [main] mapreduce.Job: Running job: job_1550764007219_0001 2019-02-21 16:08:53,438 INFO [main] mapreduce.Job: Job job_1550764007219_0001 running in uber mode : false 2019-02-21 16:08:53,440 INFO [main] mapreduce.Job: map 0% reduce 0% 2019-02-21 16:09:09,701 INFO [main] mapreduce.Job: map 1% reduce 0% 2019-02-21 16:09:12,731 INFO [main] mapreduce.Job: map 2% reduce 0% 2019-02-21 16:09:23,837 INFO [main] mapreduce.Job: map 3% reduce 0% 2019-02-21 16:09:29,911 INFO [main] mapreduce.Job: map 4% reduce 0% 2019-02-21 16:09:37,009 INFO [main] mapreduce.Job: map 5% reduce 0% 2019-02-21 16:09:45,093 INFO [main] mapreduce.Job: map 6% reduce 0% 2019-02-21 16:09:52,163 INFO [main] mapreduce.Job: map 7% reduce 0% 2019-02-21 16:09:58,249 INFO [main] mapreduce.Job: map 8% reduce 0% 2019-02-21 16:10:07,324 INFO [main] mapreduce.Job: map 9% reduce 0% 2019-02-21 16:10:14,387 INFO [main] mapreduce.Job: map 10% reduce 0% 2019-02-21 16:10:21,463 INFO [main] mapreduce.Job: map 11% reduce 0% 2019-02-21 16:10:28,522 INFO [main] mapreduce.Job: map 12% reduce 0% 2019-02-21 16:10:35,579 INFO [main] mapreduce.Job: map 13% reduce 0% 2019-02-21 16:10:42,631 INFO [main] mapreduce.Job: map 14% reduce 0% 2019-02-21 16:10:50,692 INFO [main] mapreduce.Job: map 15% reduce 0% 2019-02-21 16:10:56,743 INFO [main] mapreduce.Job: map 16% reduce 0% 2019-02-21 16:11:04,874 INFO [main] mapreduce.Job: map 17% reduce 0% 2019-02-21 16:11:11,926 INFO [main] mapreduce.Job: map 18% reduce 0% 2019-02-21 16:11:18,981 INFO [main] mapreduce.Job: map 19% reduce 0% 2019-02-21 16:11:25,027 INFO [main] mapreduce.Job: map 20% reduce 0% 2019-02-21 16:11:33,094 INFO [main] mapreduce.Job: map 21% reduce 0% 2019-02-21 16:11:40,147 INFO [main] mapreduce.Job: map 22% reduce 0% 2019-02-21 16:11:46,191 INFO [main] mapreduce.Job: map 23% reduce 0% 2019-02-21 16:11:54,241 INFO [main] mapreduce.Job: map 24% reduce 0% 2019-02-21 16:12:00,289 INFO [main] mapreduce.Job: map 25% reduce 0% 2019-02-21 16:12:07,356 INFO [main] mapreduce.Job: map 26% reduce 0% 2019-02-21 16:12:14,433 INFO [main] mapreduce.Job: map 27% reduce 0% 2019-02-21 16:12:20,507 INFO [main] mapreduce.Job: map 28% reduce 0% 2019-02-21 16:12:28,571 INFO [main] mapreduce.Job: map 29% reduce 0% 2019-02-21 16:12:36,623 INFO [main] mapreduce.Job: map 30% reduce 0% 2019-02-21 16:12:42,714 INFO [main] mapreduce.Job: map 31% reduce 0% 2019-02-21 16:12:49,769 INFO [main] mapreduce.Job: map 32% reduce 0% 2019-02-21 16:12:55,822 INFO [main] mapreduce.Job: map 33% reduce 0% 2019-02-21 16:13:03,897 INFO [main] mapreduce.Job: map 34% reduce 0% 2019-02-21 16:13:09,956 INFO [main] mapreduce.Job: map 35% reduce 0% 2019-02-21 16:13:18,023 INFO [main] mapreduce.Job: map 36% reduce 0% 2019-02-21 16:13:24,071 INFO [main] mapreduce.Job: map 37% reduce 0% 2019-02-21 16:13:32,125 INFO [main] mapreduce.Job: map 38% reduce 0% 2019-02-21 16:13:38,176 INFO [main] mapreduce.Job: map 39% reduce 0% 2019-02-21 16:13:46,225 INFO [main] mapreduce.Job: map 40% reduce 0% 2019-02-21 16:13:52,323 INFO [main] mapreduce.Job: map 41% reduce 0% 2019-02-21 16:13:59,379 INFO [main] mapreduce.Job: map 42% reduce 0% 2019-02-21 16:14:06,426 INFO [main] mapreduce.Job: map 43% reduce 0% 2019-02-21 16:14:13,466 INFO [main] mapreduce.Job: map 44% reduce 0% 2019-02-21 16:14:19,509 INFO [main] mapreduce.Job: map 45% reduce 0% 2019-02-21 16:14:27,566 INFO [main] mapreduce.Job: map 46% reduce 0% 2019-02-21 16:14:33,654 INFO [main] mapreduce.Job: map 47% reduce 0% 2019-02-21 16:14:41,740 INFO [main] mapreduce.Job: map 48% reduce 0% 2019-02-21 16:14:51,493 INFO [main] mapreduce.Job: map 49% reduce 0% 2019-02-21 16:15:04,778 INFO [main] mapreduce.Job: map 50% reduce 0% 2019-02-21 16:15:09,808 INFO [main] mapreduce.Job: map 51% reduce 0% 2019-02-21 16:15:18,890 INFO [main] mapreduce.Job: map 52% reduce 0% 2019-02-21 16:15:24,956 INFO [main] mapreduce.Job: map 53% reduce 0% 2019-02-21 16:15:34,077 INFO [main] mapreduce.Job: map 54% reduce 0% 2019-02-21 16:15:39,105 INFO [main] mapreduce.Job: map 55% reduce 0% 2019-02-21 16:15:48,249 INFO [main] mapreduce.Job: map 56% reduce 0% 2019-02-21 16:15:55,287 INFO [main] mapreduce.Job: map 57% reduce 0% 2019-02-21 16:16:03,372 INFO [main] mapreduce.Job: map 58% reduce 0% 2019-02-21 16:16:11,459 INFO [main] mapreduce.Job: map 59% reduce 0% 2019-02-21 16:16:17,511 INFO [main] mapreduce.Job: map 60% reduce 0% 2019-02-21 16:16:25,556 INFO [main] mapreduce.Job: map 61% reduce 0% 2019-02-21 16:16:33,618 INFO [main] mapreduce.Job: map 62% reduce 0% 2019-02-21 16:16:39,662 INFO [main] mapreduce.Job: map 63% reduce 0% 2019-02-21 16:16:46,707 INFO [main] mapreduce.Job: map 64% reduce 0% 2019-02-21 16:16:52,752 INFO [main] mapreduce.Job: map 65% reduce 0% 2019-02-21 16:16:59,807 INFO [main] mapreduce.Job: map 66% reduce 0% 2019-02-21 16:17:05,847 INFO [main] mapreduce.Job: map 67% reduce 0% 2019-02-21 16:17:13,906 INFO [main] mapreduce.Job: map 68% reduce 0% 2019-02-21 16:17:19,972 INFO [main] mapreduce.Job: map 69% reduce 0% 2019-02-21 16:17:28,137 INFO [main] mapreduce.Job: map 70% reduce 0% 2019-02-21 16:17:34,176 INFO [main] mapreduce.Job: map 71% reduce 0% 2019-02-21 16:17:41,239 INFO [main] mapreduce.Job: map 72% reduce 0% 2019-02-21 16:17:47,334 INFO [main] mapreduce.Job: map 73% reduce 0% 2019-02-21 16:17:55,378 INFO [main] mapreduce.Job: map 74% reduce 0% 2019-02-21 16:18:02,426 INFO [main] mapreduce.Job: map 75% reduce 0% 2019-02-21 16:18:08,466 INFO [main] mapreduce.Job: map 76% reduce 0% 2019-02-21 16:18:15,507 INFO [main] mapreduce.Job: map 77% reduce 0% 2019-02-21 16:18:23,554 INFO [main] mapreduce.Job: map 78% reduce 0% 2019-02-21 16:18:29,601 INFO [main] mapreduce.Job: map 79% reduce 0% 2019-02-21 16:18:36,652 INFO [main] mapreduce.Job: map 80% reduce 0% 2019-02-21 16:18:42,692 INFO [main] mapreduce.Job: map 81% reduce 0% 2019-02-21 16:18:50,737 INFO [main] mapreduce.Job: map 82% reduce 0% 2019-02-21 16:18:56,861 INFO [main] mapreduce.Job: map 83% reduce 0% 2019-02-21 16:19:03,915 INFO [main] mapreduce.Job: map 84% reduce 0% 2019-02-21 16:19:09,980 INFO [main] mapreduce.Job: map 85% reduce 0% 2019-02-21 16:19:17,022 INFO [main] mapreduce.Job: map 86% reduce 0% 2019-02-21 16:19:24,064 INFO [main] mapreduce.Job: map 87% reduce 0% 2019-02-21 16:19:31,103 INFO [main] mapreduce.Job: map 88% reduce 0% 2019-02-21 16:19:39,146 INFO [main] mapreduce.Job: map 89% reduce 0% 2019-02-21 16:19:44,172 INFO [main] mapreduce.Job: map 90% reduce 0% 2019-02-21 16:19:52,292 INFO [main] mapreduce.Job: map 91% reduce 0% 2019-02-21 16:19:59,339 INFO [main] mapreduce.Job: map 92% reduce 0% 2019-02-21 16:20:06,390 INFO [main] mapreduce.Job: map 93% reduce 0% 2019-02-21 16:20:13,425 INFO [main] mapreduce.Job: map 94% reduce 0% 2019-02-21 16:20:20,466 INFO [main] mapreduce.Job: map 95% reduce 0% 2019-02-21 16:20:27,505 INFO [main] mapreduce.Job: map 96% reduce 0% 2019-02-21 16:20:34,541 INFO [main] mapreduce.Job: map 97% reduce 0% 2019-02-21 16:20:41,621 INFO [main] mapreduce.Job: map 98% reduce 0% 2019-02-21 16:20:48,751 INFO [main] mapreduce.Job: map 99% reduce 0% 2019-02-21 16:20:52,770 INFO [main] mapreduce.Job: map 100% reduce 0% 2019-02-21 16:20:58,803 INFO [main] mapreduce.Job: Job job_1550764007219_0001 completed successfully 2019-02-21 16:20:58,887 INFO [main] mapreduce.Job: Counters: 42 File System Counters ABFS: Number of bytes read=551475 ABFS: Number of bytes written=0 ABFS: Number of read operations=0 ABFS: Number of large read operations=0 ABFS: Number of write operations=0 FILE: Number of bytes read=0 FILE: Number of bytes written=609808092 FILE: Number of read operations=0 FILE: Number of large read operations=0 FILE: Number of write operations=0 Job Counters Launched map tasks=3001 Data-local map tasks=2876 Rack-local map tasks=125 Total time spent by all maps in occupied slots (ms)=143239480 Total time spent by all reduces in occupied slots (ms)=0 Total time spent by all map tasks (ms)=35809870 Total vcore-milliseconds taken by all map tasks=35809870 Total megabyte-milliseconds taken by all map tasks=91673267200 Map-Reduce Framework Map input records=0 Map output records=0 Input split bytes=551475 Spilled Records=0 Failed Shuffles=0 Merged Map outputs=0 GC time elapsed (ms)=2195736 CPU time spent (ms)=7251570 Physical memory (bytes) snapshot=854513999872 Virtual memory (bytes) snapshot=7059804798976 Total committed heap usage (bytes)=640473890816 HBase Counters BYTES_IN_REMOTE_RESULTS=0 BYTES_IN_RESULTS=0 MILLIS_BETWEEN_NEXTS=2206051 NOT_SERVING_REGION_EXCEPTION=0 NUM_SCANNER_RESTARTS=0 NUM_SCAN_RESULTS_STALE=0 REGIONS_SCANNED=3001 REMOTE_RPC_CALLS=375 REMOTE_RPC_RETRIES=0 RPC_CALLS=9003 RPC_RETRIES=0 File Input Format Counters Bytes Read=0 File Output Format Counters Bytes Written=0 2019-02-21 16:21:10 [pool-1-thread-2] INFO MRExecutor:82 - ------------------------------------------------------ 2019-02-21 16:21:10 [pool-1-thread-2] INFO MRExecutor:83 - Exit value: 0 2019-02-21 16:21:10 [pool-1-thread-2] INFO MRExecutor:84 - Total time: 777.754s 2019-02-21 16:21:10 [main] INFO HadoopVariantStorageEngine:707 - ------------------------------------------------------ 2019-02-21 16:21:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:21:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:21:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:21:10 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-21 16:21:10 [main] INFO HBaseStudyConfigurationDBAdaptor:165 - Update StudyConfiguration test@GRCh37:test org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error removing files [1] from tables at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.removeFiles(HadoopVariantStorageEngine.java:731) at org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:62) at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103) at org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98) at org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34) Caused by: java.util.concurrent.ExecutionException: org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce for : "Delete from variants table" at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.removeFiles(HadoopVariantStorageEngine.java:708) ... 6 more Caused by: org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce for : "Delete from variants table" at org.opencb.opencga.storage.hadoop.variant.executors.MRExecutor.run(MRExecutor.java:87) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.lambda$removeFiles$5(HadoopVariantStorageEngine.java:671) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) opencga@a4cbf37fded8:/opt/opencga/bin$ ls

wbari commented 5 years ago

Tested with fresh installation and still fails ( not even starting MR job )

============================================== opencga@87a03708a7c0:/opt/opencga/bin$ ./opencga-analysis.sh variant remove --file ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 2019-02-26 11:25:40 [main] WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-02-26 11:25:40 [main] INFO RecoverableZooKeeper:120 - Process identifier=hconnection-0x42257bdd connecting to ZooKeeper ensemble=zk6-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181,zk1-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181,zk2-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:zookeeper.version=3.4.6-1569965, built on 02/20/2014 09:09 GMT 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:host.name=87a03708a7c0 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.version=1.8.0_201 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.vendor=Oracle Corporation 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.home=/usr/lib/jvm/java-8-oracle/jre 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.class.path=:/opt/opencga/conf/hadoop/:/opt/opencga/libs/opencga-catalog-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/biodata-models-1.4.3-20190215.140004-29.jar:/opt/opencga/libs/ga4gh-0.6.0a5.jar:/opt/opencga/libs/htsjdk-2.16.0.jar:/opt/opencga/libs/commons-jexl-2.1.1.jar:/opt/opencga/libs/ngs-java-2.9.0.jar:/opt/opencga/libs/biodata-tools-1.4.3-20190215.140034-29.jar:/opt/opencga/libs/log4j-1.2.15.jar:/opt/opencga/libs/BigWig-1.0.jar:/opt/opencga/libs/sqlite-jdbc-3.15.1.jar:/opt/opencga/libs/rocksdbjni-4.5.1.jar:/opt/opencga/libs/biojava-alignment-4.1.0.jar:/opt/opencga/libs/biojava-core-4.1.0.jar:/opt/opencga/libs/biojava-phylo-4.1.0.jar:/opt/opencga/libs/forester-1.005.jar:/opt/opencga/libs/log4j-api-2.2.jar:/opt/opencga/libs/log4j-core-2.2.jar:/opt/opencga/libs/jackson-dataformat-yaml-2.9.7.jar:/opt/opencga/libs/snakeyaml-1.23.jar:/opt/opencga/libs/jackson-dataformat-xml-2.9.7.jar:/opt/opencga/libs/woodstox-core-5.0.3.jar:/opt/opencga/libs/slf4j-api-1.7.21.jar:/opt/opencga/libs/slf4j-log4j12-1.7.21.jar:/opt/opencga/libs/mail-1.4.7.jar:/opt/opencga/libs/activation-1.1.jar:/opt/opencga/libs/commons-datastore-mongodb-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/commons-datastore-core-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/mongo-java-driver-3.7.1.jar:/opt/opencga/libs/commons-datastore-solr-3.7.3-20190118.140511-6.jar:/opt/opencga/libs/commons-lib-3.7.3-SNAPSHOT.jar:/opt/opencga/libs/jcommander-1.64.jar:/opt/opencga/libs/jackson-databind-2.9.7.jar:/opt/opencga/libs/avro-1.7.7.jar:/opt/opencga/libs/paranamer-2.3.jar:/opt/opencga/libs/snappy-java-1.0.5.jar:/opt/opencga/libs/commons-lang3-3.8.1.jar:/opt/opencga/libs/ant-1.8.2.jar:/opt/opencga/libs/ant-launcher-1.8.2.jar:/opt/opencga/libs/jersey-container-servlet-2.25.1.jar:/opt/opencga/libs/jetty-server-9.3.14.v20161028.jar:/opt/opencga/libs/javax.servlet-api-3.1.0.jar:/opt/opencga/libs/jetty-http-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-util-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-io-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-webapp-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-xml-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-servlet-9.3.14.v20161028.jar:/opt/opencga/libs/jetty-security-9.3.14.v20161028.jar:/opt/opencga/libs/jjwt-0.7.0.jar:/opt/opencga/libs/adal4j-1.6.3.jar:/opt/opencga/libs/oauth2-oidc-sdk-5.64.4.jar:/opt/opencga/libs/javax.mail-1.6.1.jar:/opt/opencga/libs/jcip-annotations-1.0-1.jar:/opt/opencga/libs/json-smart-2.3.jar:/opt/opencga/libs/accessors-smart-1.2.jar:/opt/opencga/libs/asm-5.0.4.jar:/opt/opencga/libs/lang-tag-1.4.4.jar:/opt/opencga/libs/nimbus-jose-jwt-7.0.jar:/opt/opencga/libs/gson-2.8.0.jar:/opt/opencga/libs/commons-codec-1.11.jar:/opt/opencga/libs/azure-1.13.0.jar:/opt/opencga/libs/azure-client-authentication-1.5.4.jar:/opt/opencga/libs/azure-annotations-1.2.0.jar:/opt/opencga/libs/azure-mgmt-resources-1.13.0.jar:/opt/opencga/libs/rxjava-1.2.4.jar:/opt/opencga/libs/azure-mgmt-storage-1.13.0.jar:/opt/opencga/libs/azure-mgmt-network-1.13.0.jar:/opt/opencga/libs/azure-mgmt-compute-1.13.0.jar:/opt/opencga/libs/azure-mgmt-graph-rbac-1.13.0.jar:/opt/opencga/libs/azure-mgmt-keyvault-1.13.0.jar:/opt/opencga/libs/azure-keyvault-1.0.0.jar:/opt/opencga/libs/azure-keyvault-webkey-1.0.0.jar:/opt/opencga/libs/azure-mgmt-batch-1.13.0.jar:/opt/opencga/libs/azure-mgmt-trafficmanager-1.13.0.jar:/opt/opencga/libs/azure-mgmt-dns-1.13.0.jar:/opt/opencga/libs/azure-mgmt-redis-1.13.0.jar:/opt/opencga/libs/azure-mgmt-appservice-1.13.0.jar:/opt/opencga/libs/azure-mgmt-locks-1.13.0.jar:/opt/opencga/libs/azure-mgmt-eventhub-1.13.0.jar:/opt/opencga/libs/azure-mgmt-cdn-1.13.0.jar:/opt/opencga/libs/azure-mgmt-sql-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerinstance-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerregistry-1.13.0.jar:/opt/opencga/libs/azure-mgmt-containerservice-1.13.0.jar:/opt/opencga/libs/azure-mgmt-cosmosdb-1.13.0.jar:/opt/opencga/libs/azure-mgmt-search-1.13.0.jar:/opt/opencga/libs/azure-mgmt-msi-1.13.0.jar:/opt/opencga/libs/azure-mgmt-monitor-1.13.0.jar:/opt/opencga/libs/azure-mgmt-servicebus-1.13.0.jar:/opt/opencga/libs/joda-time-2.1.jar:/opt/opencga/libs/azure-mgmt-batchai-1.13.0.jar:/opt/opencga/libs/solr-solrj-6.4.2.jar:/opt/opencga/libs/commons-io-2.5.jar:/opt/opencga/libs/httpcore-4.4.1.jar:/opt/opencga/libs/httpmime-4.4.1.jar:/opt/opencga/libs/zookeeper-3.4.6.jar:/opt/opencga/libs/stax2-api-3.1.4.jar:/opt/opencga/libs/woodstox-core-asl-4.4.1.jar:/opt/opencga/libs/noggit-0.6.jar:/opt/opencga/libs/jcl-over-slf4j-1.7.7.jar:/opt/opencga/libs/azure-batch-4.0.1.jar:/opt/opencga/libs/azure-client-runtime-1.6.4.jar:/opt/opencga/libs/client-runtime-1.6.4.jar:/opt/opencga/libs/retrofit-2.4.0.jar:/opt/opencga/libs/okhttp-3.11.0.jar:/opt/opencga/libs/logging-interceptor-3.11.0.jar:/opt/opencga/libs/okhttp-urlconnection-3.11.0.jar:/opt/opencga/libs/converter-jackson-2.4.0.jar:/opt/opencga/libs/jackson-datatype-joda-2.9.4.jar:/opt/opencga/libs/adapter-rxjava-2.4.0.jar:/opt/opencga/libs/opencga-analysis-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/hpg-bigdata-analysis-1.0.0-beta4.jar:/opt/opencga/libs/hpg-bigdata-core-1.0.0-beta4.jar:/opt/opencga/libs/bionetdb-core-0.2.0-20190131.171519-2.jar:/opt/opencga/libs/biodata-formats-1.4.3-20190215.140020-29.jar:/opt/opencga/libs/neo4j-java-driver-1.4.5.jar:/opt/opencga/libs/paxtools-core-4.3.1.jar:/opt/opencga/libs/collections-generic-4.01.jar:/opt/opencga/libs/commons-math3-3.5.jar:/opt/opencga/libs/reflections-0.9.10.jar:/opt/opencga/libs/javassist-3.19.0-GA.jar:/opt/opencga/libs/annotations-2.0.1.jar:/opt/opencga/libs/opencga-storage-app-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-server-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-storage-mongodb-1.4.0-rc3-dev.jar:/opt/opencga/libs/opencga-client-1.4.0-rc3-dev.jar:/opt/opencga/libs/jersey-client-2.25.1.jar:/opt/opencga/libs/hk2-api-2.5.0-b32.jar:/opt/opencga/libs/hk2-utils-2.5.0-b32.jar:/opt/opencga/libs/aopalliance-repackaged-2.5.0-b32.jar:/opt/opencga/libs/hk2-locator-2.5.0-b32.jar:/opt/opencga/libs/jersey-media-multipart-2.25.1.jar:/opt/opencga/libs/mimepull-1.9.6.jar:/opt/opencga/libs/protobuf-java-3.5.1.jar:/opt/opencga/libs/grpc-all-1.9.1.jar:/opt/opencga/libs/grpc-auth-1.9.1.jar:/opt/opencga/libs/google-auth-library-credentials-0.9.0.jar:/opt/opencga/libs/grpc-core-1.9.1.jar:/opt/opencga/libs/error_prone_annotations-2.1.2.jar:/opt/opencga/libs/jsr305-3.0.0.jar:/opt/opencga/libs/instrumentation-api-0.4.3.jar:/opt/opencga/libs/opencensus-api-0.10.0.jar:/opt/opencga/libs/opencensus-contrib-grpc-metrics-0.10.0.jar:/opt/opencga/libs/grpc-context-1.9.1.jar:/opt/opencga/libs/grpc-netty-1.9.1.jar:/opt/opencga/libs/netty-codec-http2-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-http-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-4.1.17.Final.jar:/opt/opencga/libs/netty-handler-4.1.17.Final.jar:/opt/opencga/libs/netty-buffer-4.1.17.Final.jar:/opt/opencga/libs/netty-common-4.1.17.Final.jar:/opt/opencga/libs/netty-handler-proxy-4.1.17.Final.jar:/opt/opencga/libs/netty-transport-4.1.17.Final.jar:/opt/opencga/libs/netty-resolver-4.1.17.Final.jar:/opt/opencga/libs/netty-codec-socks-4.1.17.Final.jar:/opt/opencga/libs/grpc-okhttp-1.9.1.jar:/opt/opencga/libs/okhttp-2.5.0.jar:/opt/opencga/libs/okio-1.13.0.jar:/opt/opencga/libs/grpc-protobuf-1.9.1.jar:/opt/opencga/libs/protobuf-java-util-3.5.1.jar:/opt/opencga/libs/proto-google-common-protos-1.0.0.jar:/opt/opencga/libs/grpc-protobuf-lite-1.9.1.jar:/opt/opencga/libs/grpc-protobuf-nano-1.9.1.jar:/opt/opencga/libs/protobuf-javanano-3.0.0-alpha-5.jar:/opt/opencga/libs/grpc-stub-1.9.1.jar:/opt/opencga/libs/grpc-testing-1.9.1.jar:/opt/opencga/libs/opencga-server-1.4.0-rc3-dev.jar:/opt/opencga/libs/jersey-media-json-jackson-2.25.1.jar:/opt/opencga/libs/jersey-entity-filtering-2.25.1.jar:/opt/opencga/libs/jackson-jaxrs-base-2.9.7.jar:/opt/opencga/libs/jackson-core-2.9.7.jar:/opt/opencga/libs/jackson-jaxrs-json-provider-2.9.7.jar:/opt/opencga/libs/jackson-module-jaxb-annotations-2.9.7.jar:/opt/opencga/libs/swagger-jersey2-jaxrs-1.5.21.jar:/opt/opencga/libs/swagger-jaxrs-1.5.21.jar:/opt/opencga/libs/swagger-core-1.5.21.jar:/opt/opencga/libs/swagger-models-1.5.21.jar:/opt/opencga/libs/swagger-annotations-1.5.21.jar:/opt/opencga/libs/jersey-container-servlet-core-2.25.1.jar:/opt/opencga/libs/javax.inject-2.5.0-b32.jar:/opt/opencga/libs/jersey-common-2.25.1.jar:/opt/opencga/libs/javax.annotation-api-1.2.jar:/opt/opencga/libs/jersey-guava-2.25.1.jar:/opt/opencga/libs/osgi-resource-locator-1.0.1.jar:/opt/opencga/libs/jersey-server-2.25.1.jar:/opt/opencga/libs/jersey-media-jaxb-2.25.1.jar:/opt/opencga/libs/validation-api-1.1.0.Final.jar:/opt/opencga/libs/javax.ws.rs-api-2.0.1.jar:/opt/opencga/libs/cellbase-client-4.6.2-20190109.100231-2.jar:/opt/opencga/libs/cellbase-core-4.6.2-SNAPSHOT.jar:/opt/opencga/libs/cellbase-lib-4.6.2-SNAPSHOT.jar:/opt/opencga/libs/redisson-2.2.0.jar:/opt/opencga/libs/reactor-stream-2.0.7.RELEASE.jar:/opt/opencga/libs/reactor-core-2.0.7.RELEASE.jar:/opt/opencga/libs/reactive-streams-1.0.0.jar:/opt/opencga/libs/jackson-dataformat-cbor-2.6.3.jar:/opt/opencga/libs/kryo-2.23.0.jar:/opt/opencga/libs/minlog-1.2.jar:/opt/opencga/libs/objenesis-2.1.jar:/opt/opencga/libs/httpclient-4.3.4.jar:/opt/opencga/libs/commons-logging-1.1.3.jar:/opt/opencga/libs/jackson-annotations-2.9.7.jar:/opt/opencga/libs/hamcrest-core-1.3.jar:/opt/opencga/libs/opencga-storage-hadoop-core-1.4.0-rc3-dev.jar:/opt/opencga/libs/guava-19.0.jar:/opt/opencga/libs/opencga-storage-hadoop-deps-1.4.0-rc3-dev-hdp-2.6.5-shaded.jar:/opt/opencga/libs/htrace-core-3.1.0-incubating.jar:/opt/opencga/libs/commons-cli-1.2.jar:/opt/opencga/libs/avro-ipc-1.7.7.jar:/opt/opencga/libs/netty-3.4.0.Final.jar:/opt/opencga/libs/velocity-1.7.jar:/opt/opencga/libs/avro-mapred-1.7.7-hadoop2.jar:/opt/opencga/libs/avro-ipc-1.7.7-tests.jar:/opt/opencga/libs/commons-configuration-1.6.jar:/opt/opencga/libs/commons-digester-1.8.jar:/opt/opencga/libs/commons-beanutils-1.7.0.jar:/opt/opencga/libs/commons-beanutils-core-1.8.0.jar:/opt/opencga/libs/commons-lang-2.6.jar:/opt/opencga/libs/commons-net-3.1.jar:/opt/opencga/libs/commons-httpclient-3.1.jar:/opt/opencga/libs/curator-recipes-2.7.1.jar:/opt/opencga/libs/curator-client-2.7.1.jar:/opt/opencga/libs/curator-framework-2.7.1.jar:/opt/opencga/libs/leveldbjni-all-1.8.jar:/opt/opencga/libs/apacheds-kerberos-codec-2.0.0-M15.jar:/opt/opencga/libs/apacheds-i18n-2.0.0-M15.jar:/opt/opencga/libs/api-asn1-api-1.0.0-M20.jar:/opt/opencga/libs/api-util-1.0.0-M20.jar:/opt/opencga/libs/azure-storage-2.0.0.jar:/opt/opencga/libs/jetty-util-6.1.26.jar:/opt/opencga/libs/disruptor-3.3.0.jar:/opt/opencga/libs/metrics-core-2.2.0.jar:/opt/opencga/libs/commons-math-2.2.jar:/opt/opencga/libs/commons-compress-1.4.1.jar:/opt/opencga/libs/xz-1.0.jar:/opt/opencga/libs/netty-all-4.0.23.Final.jar:/opt/opencga/libs/jamon-runtime-2.4.1.jar:/opt/opencga/libs/jackson-core-asl-1.9.13.jar:/opt/opencga/libs/jackson-mapper-asl-1.9.13.jar:/opt/opencga/libs/jackson-jaxrs-1.9.13.jar:/opt/opencga/libs/jackson-xc-1.9.13.jar:/opt/opencga/libs/antlr-runtime-3.5.2.jar:/opt/opencga/libs/jline-2.11.jar:/opt/opencga/libs/sqlline-1.1.9.jar:/opt/opencga/libs/tephra-api-0.7.0.jar:/opt/opencga/libs/tephra-core-0.7.0.jar:/opt/opencga/libs/guice-3.0.jar:/opt/opencga/libs/javax.inject-1.jar:/opt/opencga/libs/aopalliance-1.0.jar:/opt/opencga/libs/guice-assistedinject-3.0.jar:/opt/opencga/libs/libthrift-0.9.0.jar:/opt/opencga/libs/fastutil-6.5.6.jar:/opt/opencga/libs/twill-common-0.6.0-incubating.jar:/opt/opencga/libs/twill-core-0.6.0-incubating.jar:/opt/opencga/libs/twill-api-0.6.0-incubating.jar:/opt/opencga/libs/asm-all-5.0.2.jar:/opt/opencga/libs/twill-discovery-api-0.6.0-incubating.jar:/opt/opencga/libs/twill-discovery-core-0.6.0-incubating.jar:/opt/opencga/libs/twill-zookeeper-0.6.0-incubating.jar:/opt/opencga/libs/metrics-core-3.1.0.jar:/opt/opencga/libs/tephra-hbase-compat-1.1-0.7.0.jar:/opt/opencga/libs/snappy-0.3.jar:/opt/opencga/libs/commons-collections-3.2.1.jar:/opt/opencga/libs/commons-csv-1.0.jar:/opt/opencga/libs/parquet-avro-1.7.0.jar:/opt/opencga/libs/parquet-column-1.7.0.jar:/opt/opencga/libs/parquet-common-1.7.0.jar:/opt/opencga/libs/parquet-encoding-1.7.0.jar:/opt/opencga/libs/parquet-generator-1.7.0.jar:/opt/opencga/libs/parquet-hadoop-1.7.0.jar:/opt/opencga/libs/parquet-jackson-1.7.0.jar:/opt/opencga/libs/parquet-format-2.3.0-incubating.jar:/opt/opencga/libs/opencga-app-1.4.0-rc3-dev.jar 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.io.tmpdir=/tmp 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:java.compiler= 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:os.name=Linux 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:os.arch=amd64 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:os.version=4.18.0-1011-azure 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:user.name=opencga 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:user.home=/home/opencga 2019-02-26 11:25:40 [main] INFO ZooKeeper:100 - Client environment:user.dir=/opt/opencga/bin 2019-02-26 11:25:40 [main] INFO ZooKeeper:438 - Initiating client connection, connectString=zk6-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181,zk1-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181,zk2-cgahba.hhm4yxt2jm1ujkk4pjngiah14h.fx.internal.cloudapp.net:2181 sessionTimeout=120000 watcher=org.apache.hadoop.hbase.zookeeper.PendingWatcher@5a021cb9 2019-02-26 11:25:40 [main-SendThread(10.0.0.8:2181)] INFO ClientCnxn:975 - Opening socket connection to server 10.0.0.8/10.0.0.8:2181. Will not attempt to authenticate using SASL (unknown error) 2019-02-26 11:25:40 [main-SendThread(10.0.0.8:2181)] INFO ClientCnxn:852 - Socket connection established to 10.0.0.8/10.0.0.8:2181, initiating session 2019-02-26 11:25:40 [main-SendThread(10.0.0.8:2181)] INFO ClientCnxn:1235 - Session establishment complete on server 10.0.0.8/10.0.0.8:2181, sessionid = 0x169255acc5c0458, negotiated timeout = 120000 2019-02-26 11:25:40 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:40 [main] WARN DynamicClassLoader:120 - Failed to identify the fs of dir /hbase/lib, ignored Cannot run program "/usr/lib/hdinsight-common/scripts/decrypt.sh": error=2, No such file or directory at org.apache.hadoop.fs.azurebfs.services.ShellDecryptionKeyProvider.getStorageAccountKey(ShellDecryptionKeyProvider.java:65) at org.apache.hadoop.fs.azurebfs.AbfsConfiguration.getStorageAccountKey(AbfsConfiguration.java:355) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystemStore.initializeClient(AzureBlobFileSystemStore.java:880) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystemStore.(AzureBlobFileSystemStore.java:181) at org.apache.hadoop.fs.azurebfs.AzureBlobFileSystem.initialize(AzureBlobFileSystem.java:108) at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2796) at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:99) at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2830) at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2812) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:390) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:179) at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:374) at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295) at org.apache.hadoop.hbase.util.DynamicClassLoader.initTempDir(DynamicClassLoader.java:118) at org.apache.hadoop.hbase.util.DynamicClassLoader.(DynamicClassLoader.java:98) at org.apache.hadoop.hbase.protobuf.ProtobufUtil.(ProtobufUtil.java:251) at org.apache.hadoop.hbase.ClusterId.parseFrom(ClusterId.java:64) at org.apache.hadoop.hbase.zookeeper.ZKClusterId.readClusterIdZNode(ZKClusterId.java:75) at org.apache.hadoop.hbase.client.ZooKeeperRegistry.getClusterId(ZooKeeperRegistry.java:105) at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.retrieveClusterId(ConnectionManager.java:903) at org.apache.hadoop.hbase.client.ConnectionManager$HConnectionImplementation.(ConnectionManager.java:648) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:238) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:218) at org.apache.hadoop.hbase.client.ConnectionFactory.createConnection(ConnectionFactory.java:119) at org.opencb.opencga.storage.hadoop.utils.HBaseManager.getConnection(HBaseManager.java:124) at org.opencb.opencga.storage.hadoop.utils.HBaseManager.(HBaseManager.java:78) at org.opencb.opencga.storage.hadoop.variant.metadata.AbstractHBaseDBAdaptor.(AbstractHBaseDBAdaptor.java:48) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseProjectMetadataDBAdaptor.(HBaseProjectMetadataDBAdaptor.java:46) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:38) at org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:13) at org.opencb.opencga.storage.core.metadata.StudyConfigurationManager.(StudyConfigurationManager.java:77) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.getStudyConfigurationManager(HadoopVariantStorageEngine.java:922) at org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation.updateCatalogFromStudyConfiguration(StorageOperation.java:117) at org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:40) at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103) at org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98) at org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34) 2019-02-26 11:25:40 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:40 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:40 [main] INFO HBaseManager:128 - Opened Hadoop DB connection hconnection-0x42257bdd called from [java.lang.Thread.getStackTrace(Thread.java:1559), org.opencb.opencga.storage.hadoop.utils.HBaseManager.getConnection(HBaseManager.java:127), org.opencb.opencga.storage.hadoop.utils.HBaseManager.(HBaseManager.java:78), org.opencb.opencga.storage.hadoop.variant.metadata.AbstractHBaseDBAdaptor.(AbstractHBaseDBAdaptor.java:48), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseProjectMetadataDBAdaptor.(HBaseProjectMetadataDBAdaptor.java:46), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:38), org.opencb.opencga.storage.hadoop.variant.metadata.HBaseVariantStorageMetadataDBAdaptorFactory.buildProjectMetadataDBAdaptor(HBaseVariantStorageMetadataDBAdaptorFactory.java:13), org.opencb.opencga.storage.core.metadata.StudyConfigurationManager.(StudyConfigurationManager.java:77), org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.getStudyConfigurationManager(HadoopVariantStorageEngine.java:922), org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation.updateCatalogFromStudyConfiguration(StorageOperation.java:117), org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:40), org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241), org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264), org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103), org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98), org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34)] 2019-02-26 11:25:41 [main] INFO CatalogStudyConfigurationFactory:104 - Updating StudyConfiguration 1 2019-02-26 11:25:41 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:42 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] INFO HBaseStudyConfigurationDBAdaptor:165 - Update StudyConfiguration test@GRCh37:test 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:25:43 [main] INFO HadoopVariantStorageEngine:653 - ------------------------------------------------------ 2019-02-26 11:25:43 [main] INFO HadoopVariantStorageEngine:654 - Remove files [1] in archive 'opencga_test_GRCh37_archive_1' and analysis table 'opencga_test_GRCh37_variants' 2019-02-26 11:25:43 [main] INFO HadoopVariantStorageEngine:655 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-1] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-1] INFO MRExecutor:79 - Delete from variants table 2019-02-26 11:25:43 [pool-1-thread-1] INFO MRExecutor:80 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-2] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-2] INFO MRExecutor:79 - Delete from archive table 2019-02-26 11:25:43 [pool-1-thread-2] INFO MRExecutor:80 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-3] INFO MRExecutor:78 - ------------------------------------------------------ 2019-02-26 11:25:43 [pool-1-thread-3] INFO MRExecutor:79 - Delete from SamplesIndex table 2019-02-26 11:25:43 [pool-1-thread-3] INFO MRExecutor:80 - ------------------------------------------------------ Connect to Hadoop edge node sshuser@cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net sshpass -e ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60 sshuser@cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net Connect to Hadoop edge node sshuser@cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net sshpass -e ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o ServerAliveInterval=60 sshuser@cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net Warning: Permanently added 'cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net,13.74.164.33' (ECDSA) to the list of known hosts. Warning: Permanently added 'cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net,13.74.164.33' (ECDSA) to the list of known hosts. Authorized uses only. All activity may be monitored and reported. Authorized uses only. All activity may be monitored and reported. 2019-02-26 11:26:02,034 INFO [main] utils.AbstractHBaseDriver: [opencga_test_GRCh37_variants, columns_to_delete, 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database.name, opencga, dbadaptor.phoenix.fetch_size, -1, annotator, cellbase_rest, annotator.cellbase.exclude, expression, annotator.cellbase.use_cache, true, annotator.cellbase.imprecise_variants, false, opencga.storage.hadoop.jar-with-dependencies, opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar, opencga.archive.chunk_size, 1000, hadoop.load.archive.batch.size, 3, hadoop.load.variant.batch.size, 500, opencga.archive.table.presplit.size, 500, opencga.archive.table.compression, gz, opencga.variant.table.presplit.size, 500, opencga.variant.table.compression, snappy, opencga.sample-index.table.presplit.size, 15, opencga.sample-index.table.compression, snappy, intersect.active, true, intersect.always, false, intersect.params.threshold, 3, opencga.hadoop.bin, hadoop, opencga.mr.executor, ssh, mapreduce.map.cpu.vcores, 1, mapreduce.map.memory.mb, 2560, opencga.variant.table.mapreduce.map.java.opts, -Xmx2048m,-XX:+UseG1GC,-Djava.util.concurrent.ForkJoinPool.common.parallelism=1, opencga.storage.hadoop.hbase.merge.archive.scan.batchsize, 2000, opencga.storage.hadoop.mapreduce.scanner.timeout, 300000, opencga.mr.executor.ssh.host, cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net, opencga.mr.executor.ssh.user, sshuser, opencga.mr.executor.ssh.password, f1d5971-d266-4113-adf1-212aeb6409bH, opencga.mr.executor.ssh.remote_opencga_home, /home/sshuser/opencga/, resume, false, opencga.variant.table.timestamp, 1551180343263, delete.hbase.column.mapper.class, org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine] 2019-02-26 11:26:02,199 INFO [main] utils.AbstractHBaseDriver: [opencga_test_GRCh37_archive_1, columns_to_delete, 0:1_R,0:1_N, database.name, opencga, dbadaptor.phoenix.fetch_size, -1, annotator, cellbase_rest, annotator.cellbase.exclude, expression, annotator.cellbase.use_cache, true, annotator.cellbase.imprecise_variants, false, opencga.storage.hadoop.jar-with-dependencies, opencga-storage-hadoop-core-1.4.0-rc3-dev-jar-with-dependencies.jar, opencga.archive.chunk_size, 1000, hadoop.load.archive.batch.size, 3, hadoop.load.variant.batch.size, 500, opencga.archive.table.presplit.size, 500, opencga.archive.table.compression, gz, opencga.variant.table.presplit.size, 500, opencga.variant.table.compression, snappy, opencga.sample-index.table.presplit.size, 15, opencga.sample-index.table.compression, snappy, intersect.active, true, intersect.always, false, intersect.params.threshold, 3, opencga.hadoop.bin, hadoop, opencga.mr.executor, ssh, mapreduce.map.cpu.vcores, 1, mapreduce.map.memory.mb, 2560, opencga.variant.table.mapreduce.map.java.opts, -Xmx2048m,-XX:+UseG1GC,-Djava.util.concurrent.ForkJoinPool.common.parallelism=1, opencga.storage.hadoop.hbase.merge.archive.scan.batchsize, 2000, opencga.storage.hadoop.mapreduce.scanner.timeout, 300000, opencga.mr.executor.ssh.host, cgahbasefy7mp33ww7dbs-ssh.azurehdinsight.net, opencga.mr.executor.ssh.user, sshuser, opencga.mr.executor.ssh.password, f1d5971-d266-4113-adf1-212aeb6409bH, opencga.mr.executor.ssh.remote_opencga_home, /home/sshuser/opencga/, resume, false, opencga.variant.table.timestamp, 1551180343263, delete.hbase.column.mapper.class, org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine] 2019-02-26 11:26:02,325 INFO [main] utils.DeleteHBaseColumnDriver: Scan set Caching to 100 2019-02-26 11:26:02,477 INFO [main] utils.DeleteHBaseColumnDriver: Scan set Caching to 100 2019-02-26 11:26:02,530 ERROR [main] utils.DeleteHBaseColumnDriver: Error executing class org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver java.lang.RuntimeException: java.lang.RuntimeException: class org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine not org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver$DeleteHBaseColumnMapper at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2340) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.setupJob(DeleteHBaseColumnDriver.java:80) at org.opencb.opencga.storage.hadoop.utils.AbstractHBaseDriver.run(AbstractHBaseDriver.java:97) at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:76) at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:90) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.privateMain(DeleteHBaseColumnDriver.java:189) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.main(DeleteHBaseColumnDriver.java:177) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.hadoop.util.RunJar.run(RunJar.java:243) at org.apache.hadoop.util.RunJar.main(RunJar.java:158) Caused by: java.lang.RuntimeException: class org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine not org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver$DeleteHBaseColumnMapper at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2334) ... 12 more 2019-02-26 11:26:02,652 ERROR [main] utils.DeleteHBaseColumnDriver: Error executing class org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver java.lang.RuntimeException: java.lang.RuntimeException: class org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine not org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver$DeleteHBaseColumnMapper at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2340) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.setupJob(DeleteHBaseColumnDriver.java:80) at org.opencb.opencga.storage.hadoop.utils.AbstractHBaseDriver.run(AbstractHBaseDriver.java:97) at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:76) at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:90) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.privateMain(DeleteHBaseColumnDriver.java:189) at org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver.main(DeleteHBaseColumnDriver.java:177) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.hadoop.util.RunJar.run(RunJar.java:243) at org.apache.hadoop.util.RunJar.main(RunJar.java:158) Caused by: java.lang.RuntimeException: class org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine not org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver$DeleteHBaseColumnMapper at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2334) ... 12 more 2019-02-26 11:26:11 [pool-1-thread-1] INFO MRExecutor:82 - ------------------------------------------------------ 2019-02-26 11:26:11 [pool-1-thread-1] INFO MRExecutor:83 - Exit value: 1 2019-02-26 11:26:11 [pool-1-thread-1] INFO MRExecutor:84 - Total time: 27.385s 2019-02-26 11:26:13 [pool-1-thread-2] INFO MRExecutor:82 - ------------------------------------------------------ 2019-02-26 11:26:13 [pool-1-thread-2] INFO MRExecutor:83 - Exit value: 1 2019-02-26 11:26:13 [pool-1-thread-2] INFO MRExecutor:84 - Total time: 30.055s 2019-02-26 11:26:13 [main] INFO HadoopVariantStorageEngine:707 - ------------------------------------------------------ 2019-02-26 11:26:13 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:26:13 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:26:13 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:26:13 [main] WARN Configuration:2825 - hbase-site.xml:an attempt to override final parameter: dfs.support.append; Ignoring. 2019-02-26 11:26:14 [main] INFO HBaseStudyConfigurationDBAdaptor:165 - Update StudyConfiguration test@GRCh37:test org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error removing files [1] from tables at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.removeFiles(HadoopVariantStorageEngine.java:731) at org.opencb.opencga.storage.core.manager.variant.operations.VariantRemoveStorageOperation.removeFiles(VariantRemoveStorageOperation.java:62) at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.removeFile(VariantStorageManager.java:241) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.remove(VariantCommandExecutor.java:264) at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:103) at org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:98) at org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:34) Caused by: java.util.concurrent.ExecutionException: org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce for : "Delete from variants table" at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.removeFiles(HadoopVariantStorageEngine.java:708) ... 6 more Caused by: org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce for : "Delete from variants table" at org.opencb.opencga.storage.hadoop.variant.executors.MRExecutor.run(MRExecutor.java:87) at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.lambda$removeFiles$5(HadoopVariantStorageEngine.java:671) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

wbari commented 5 years ago

2019-02-26 11:26:02,530 ERROR [main] utils.DeleteHBaseColumnDriver: Error executing class org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver java.lang.RuntimeException: java.lang.RuntimeException: class org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine not org.opencb.opencga.storage.hadoop.utils.DeleteHBaseColumnDriver$DeleteHBaseColumnMapper