{"id":6419,"date":"2014-04-17T13:33:24","date_gmt":"2014-04-17T13:33:24","guid":{"rendered":"https:\/\/unknownerror.org\/index.php\/2014\/04\/17\/zookeeper-error-connection-loss-exception-collection-of-common-programming-errors\/"},"modified":"2014-04-17T13:33:24","modified_gmt":"2014-04-17T13:33:24","slug":"zookeeper-error-connection-loss-exception-collection-of-common-programming-errors","status":"publish","type":"post","link":"https:\/\/unknownerror.org\/index.php\/2014\/04\/17\/zookeeper-error-connection-loss-exception-collection-of-common-programming-errors\/","title":{"rendered":"Zookeeper error connection loss exception-Collection of common programming errors"},"content":{"rendered":"<p>I&#8217;m running a SeqWare VM on an amazon EC2 instance I&#8217;m trying to use the SeqWare query engine to query data from VCF files. When I first launch the instance and follow the instructions to import data, It works fine, and continues to work until I stop the instance. When I restart it. It won&#8217;t let me import anything, nor create a new workspace. It always returns the error below. I looked at the processes and found that none of the required nodes were running, so I logged into root and went to the <code>etc\/init.d<\/code> directory and start everything again, at which point, when T try to import data, I don&#8217;t even get an error and I have to stop the process.<\/p>\n<pre><code>[seqware@master target]$ java -classpath seqware-distribution-0.13.6.7-qe-full.jar com.github.seqware.queryengine.system.importers.SOFeatureImporter -i ..\/..\/seqware-queryengine\/src\/test\/resources\/com\/github\/seqware\/queryengine\/system\/FeatureImporter\/consequences_annotated.vcf ALL.chr3.phase1_release_v3.20101123.snps_indels_svs.genotypes.3_100001-101000.vcf -o keyValueVCF.out -r hg_19 -s c111aea5-5e18-4c62-a8a7-ec82fe151301 -a ad_hoc -w VCFVariantImportWorker                 \n[SeqWare Query Engine] 0    [main] ERROR org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper  - ZooKeeper exists failed after 3 retries\n[SeqWare Query Engine] 1    [main] ERROR org.apache.hadoop.hbase.zookeeper.ZooKeeperWatcher  - hconnection Received unexpected KeeperException, re-throwing exception\norg.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for \/hbase\/master\n        at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)\n        at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)\n        at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)\n        at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)\n        at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)\n        at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)\n        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)\n        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.(HConnectionManager.java:569)\n        at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)\n        at org.apache.hadoop.hbase.client.HBaseAdmin.(HBaseAdmin.java:100)\n        at com.github.seqware.queryengine.impl.HBaseStorage.(HBaseStorage.java:89)\n        at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)\n        at com.github.seqware.queryengine.impl.SimpleModelManager.(SimpleModelManager.java:49)\n        at com.github.seqware.queryengine.impl.HBaseModelManager.(HBaseModelManager.java:36)\n        at com.github.seqware.queryengine.impl.MRHBaseModelManager.(MRHBaseModelManager.java:32)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)\n        at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)\n        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)\n        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)\n[SeqWare Query Engine] 3    [main] FATAL org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation  - Unexpected exception during initialization, aborting\norg.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for \/hbase\/master\n        at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)\n        at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)\n        at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)\n        at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)\n        at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)\n        at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)\n        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)\n        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.(HConnectionManager.java:569)\n        at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)\n        at org.apache.hadoop.hbase.client.HBaseAdmin.(HBaseAdmin.java:100)\n        at com.github.seqware.queryengine.impl.HBaseStorage.(HBaseStorage.java:89)\n        at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)\n        at com.github.seqware.queryengine.impl.SimpleModelManager.(SimpleModelManager.java:49)\n        at com.github.seqware.queryengine.impl.HBaseModelManager.(HBaseModelManager.java:36)\n        at com.github.seqware.queryengine.impl.MRHBaseModelManager.(MRHBaseModelManager.java:32)\n        at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)\n        at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)\n        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)\n        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>I&#8217;m running a SeqWare VM on an amazon EC2 instance I&#8217;m trying to use the SeqWare query engine to query data from VCF files. When I first launch the instance and follow the instructions to import data, It works fine, and continues to work until I stop the instance. When I restart it. It won&#8217;t [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-6419","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts\/6419","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/comments?post=6419"}],"version-history":[{"count":0,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/posts\/6419\/revisions"}],"wp:attachment":[{"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/media?parent=6419"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/categories?post=6419"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/unknownerror.org\/index.php\/wp-json\/wp\/v2\/tags?post=6419"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}