Zookeeper error connection loss exception-Collection of common programming errors

I’m running a SeqWare VM on an amazon EC2 instance I’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’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 etc/init.d directory and start everything again, at which point, when T try to import data, I don’t even get an error and I have to stop the process.

[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                 
[SeqWare Query Engine] 0    [main] ERROR org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper  - ZooKeeper exists failed after 3 retries
[SeqWare Query Engine] 1    [main] ERROR org.apache.hadoop.hbase.zookeeper.ZooKeeperWatcher  - hconnection Received unexpected KeeperException, re-throwing exception
org.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for /hbase/master
        at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)
        at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)
        at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)
        at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)
        at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)
        at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)
        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)
        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.(HConnectionManager.java:569)
        at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)
        at org.apache.hadoop.hbase.client.HBaseAdmin.(HBaseAdmin.java:100)
        at com.github.seqware.queryengine.impl.HBaseStorage.(HBaseStorage.java:89)
        at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)
        at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)
        at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)
        at com.github.seqware.queryengine.impl.SimpleModelManager.(SimpleModelManager.java:49)
        at com.github.seqware.queryengine.impl.HBaseModelManager.(HBaseModelManager.java:36)
        at com.github.seqware.queryengine.impl.MRHBaseModelManager.(MRHBaseModelManager.java:32)
        at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)
        at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)
        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)
        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)
[SeqWare Query Engine] 3    [main] FATAL org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation  - Unexpected exception during initialization, aborting
org.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for /hbase/master
        at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)
        at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)
        at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)
        at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)
        at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)
        at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)
        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)
        at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.(HConnectionManager.java:569)
        at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)
        at org.apache.hadoop.hbase.client.HBaseAdmin.(HBaseAdmin.java:100)
        at com.github.seqware.queryengine.impl.HBaseStorage.(HBaseStorage.java:89)
        at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)
        at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)
        at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)
        at com.github.seqware.queryengine.impl.SimpleModelManager.(SimpleModelManager.java:49)
        at com.github.seqware.queryengine.impl.HBaseModelManager.(HBaseModelManager.java:36)
        at com.github.seqware.queryengine.impl.MRHBaseModelManager.(MRHBaseModelManager.java:32)
        at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)
        at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)
        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)
        at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)