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**coldturkey** · 04-11-2013, 03:07 PM

brian@brian-XPS-L521X[scripts] cd /opt/smrtanalysis/etc/scripts && bash dbdata.sh [ 9:05AM]
Apr 12, 2013 9:05:29 AM com.pacbio.secondary.smrtportal.dbupdate.InitDbData <init>
INFO: Inserting required smrtportal data...
Apr 12, 2013 9:05:29 AM com.pacbio.secondary.smrtportal.common.entities.EntityUtil getEntityManager
INFO: Initializing EntityManagerFactory: smrtportal
2 [main] INFO org.hibernate.cfg.annotations.Version - Hibernate Annotations 3.5.5-Final
11 [main] INFO org.hibernate.cfg.Environment - Hibernate 3.5.5-Final
12 [main] INFO org.hibernate.cfg.Environment - hibernate.properties not found
15 [main] INFO org.hibernate.cfg.Environment - Bytecode provider name : javassist
17 [main] INFO org.hibernate.cfg.Environment - using JDK 1.4 java.sql.Timestamp handling
79 [main] INFO org.hibernate.annotations.common.Version - Hibernate Commons Annotations 3.2.0.Final
84 [main] INFO org.hibernate.ejb.Version - Hibernate EntityManager 3.5.5-Final
350 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.UserGroup
369 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.UserGroup on table UserGroup
410 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobInput
411 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobInput on table JobInput
413 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.Input
414 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.Input on table Input
432 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobStatus
432 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobStatus on table JobStatus
436 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.InputGroup
437 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.InputGroup on table InputGroup
439 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.User
440 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.User on table User
449 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobGroup
449 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobGroup on table JobGroup
452 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.SmrtGroup
452 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.SmrtGroup on table SmrtGroup
455 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.Job
455 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.Job on table Job
468 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.CustomField
468 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.CustomField on table CustomField
474 [main] INFO org.hibernate.cfg.AnnotationConfiguration - Hibernate Validator not found: ignoring
516 [main] INFO org.hibernate.cfg.search.HibernateSearchEventListenerRegister - Unable to find org.hibernate.search.event.FullTextIndexEventListener on the classpath. Hibernate Search is not enabled.
546 [main] INFO org.hibernate.connection.ConnectionProviderFactory - Initializing connection provider: org.hibernate.connection.C3P0ConnectionProvider
547 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - C3P0 using driver: com.mysql.jdbc.Driver at URL: jdbc:mysql://localhost:3306/smrtportal?zeroDateTimeBehavior=convertToNull&useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&
548 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - Connection properties: {user=smrtportal, password=****, autocommit=true, release_mode=auto}
548 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - autocommit mode: true
Apr 12, 2013 9:05:30 AM com.mchange.v2.log.MLog <clinit>
INFO: MLog clients using java 1.4+ standard logging.
Apr 12, 2013 9:05:30 AM com.mchange.v2.c3p0.C3P0Registry banner
INFO: Initializing c3p0-0.9.1 [built 16-January-2007 14:46:42; debug? true; trace: 10]
Apr 12, 2013 9:05:30 AM com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource getPoolManager
INFO: Initializing c3p0 pool... com.mchange.v2.c3p0.PoolBackedDataSource@629733f4 [ connectionPoolDataSource -> com.mchange.v2.c3p0.WrapperConnectionPoolDataSource@93c228b [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, debugUnreturnedConnectionStackTraces -> false, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> z8kfsx8t1xqmr2a1d585rz|124f5739, idleConnectionTestPeriod -> 0, initialPoolSize -> 3, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, nestedDataSource -> com.mchange.v2.c3p0.DriverManagerDataSource@c262f21 [ description -> null, driverClass -> null, factoryClassLocation -> null, identityToken -> z8kfsx8t1xqmr2a1d585rz|2504df84, jdbcUrl -> jdbc:mysql://localhost:3306/smrtportal?zeroDateTimeBehavior=convertToNull&useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&, properties -> {user=******, password=******, autocommit=true, release_mode=auto} ], preferredTestQuery -> null, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false; userOverrides: {} ], dataSourceName -> null, factoryClassLocation -> null, identityToken -> z8kfsx8t1xqmr2a1d585rz|4cd062fa, numHelperThreads -> 3 ]
922 [main] INFO org.hibernate.cfg.SettingsFactory - RDBMS: MySQL, version: 5.5.29-0ubuntu0.12.04.2
922 [main] INFO org.hibernate.cfg.SettingsFactory - JDBC driver: MySQL-AB JDBC Driver, version: mysql-connector-java-5.1.14 ( Revision: ${bzr.revision-id} )
937 [main] INFO org.hibernate.dialect.Dialect - Using dialect: org.hibernate.dialect.MySQLDialect
940 [main] INFO org.hibernate.engine.jdbc.JdbcSupportLoader - Disabling contextual LOB creation as createClob() method threw error : java.lang.reflect.InvocationTargetException
941 [main] INFO org.hibernate.transaction.TransactionFactoryFactory - Transaction strategy: org.hibernate.transaction.JDBCTransactionFactory
942 [main] INFO org.hibernate.transaction.TransactionManagerLookupFactory - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
942 [main] INFO org.hibernate.cfg.SettingsFactory - Automatic flush during beforeCompletion(): disabled
942 [main] INFO org.hibernate.cfg.SettingsFactory - Automatic session close at end of transaction: disabled
942 [main] INFO org.hibernate.cfg.SettingsFactory - JDBC batch size: 15
942 [main] INFO org.hibernate.cfg.SettingsFactory - JDBC batch updates for versioned data: disabled
942 [main] INFO org.hibernate.cfg.SettingsFactory - Scrollable result sets: enabled
942 [main] INFO org.hibernate.cfg.SettingsFactory - JDBC3 getGeneratedKeys(): enabled
942 [main] INFO org.hibernate.cfg.SettingsFactory - Connection release mode: auto
943 [main] INFO org.hibernate.cfg.SettingsFactory - Maximum outer join fetch depth: 2
943 [main] INFO org.hibernate.cfg.SettingsFactory - Default batch fetch size: 1
943 [main] INFO org.hibernate.cfg.SettingsFactory - Generate SQL with comments: disabled
943 [main] INFO org.hibernate.cfg.SettingsFactory - Order SQL updates by primary key: disabled
943 [main] INFO org.hibernate.cfg.SettingsFactory - Order SQL inserts for batching: disabled
943 [main] INFO org.hibernate.cfg.SettingsFactory - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
944 [main] INFO org.hibernate.hql.ast.ASTQueryTranslatorFactory - Using ASTQueryTranslatorFactory
944 [main] INFO org.hibernate.cfg.SettingsFactory - Query language substitutions: {}
944 [main] INFO org.hibernate.cfg.SettingsFactory - JPA-QL strict compliance: enabled
944 [main] INFO org.hibernate.cfg.SettingsFactory - Second-level cache: enabled
944 [main] INFO org.hibernate.cfg.SettingsFactory - Query cache: disabled
944 [main] INFO org.hibernate.cfg.SettingsFactory - Cache region factory : org.hibernate.cache.impl.NoCachingRegionFactory
944 [main] INFO org.hibernate.cfg.SettingsFactory - Optimize cache for minimal puts: disabled
944 [main] INFO org.hibernate.cfg.SettingsFactory - Structured second-level cache entries: disabled
947 [main] INFO org.hibernate.cfg.SettingsFactory - Statistics: disabled
947 [main] INFO org.hibernate.cfg.SettingsFactory - Deleted entity synthetic identifier rollback: disabled
947 [main] INFO org.hibernate.cfg.SettingsFactory - Default entity-mode: pojo
947 [main] INFO org.hibernate.cfg.SettingsFactory - Named query checking : enabled
947 [main] INFO org.hibernate.cfg.SettingsFactory - Check Nullability in Core (should be disabled when Bean Validation is on): enabled
978 [main] INFO org.hibernate.impl.SessionFactoryImpl - building session factory
1184 [main] INFO org.hibernate.impl.SessionFactoryObjectFactory - Not binding factory to JNDI, no JNDI name configured
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.dbupdate.InitDbData <init>
INFO: group 'all' already exists.
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.helpers.UserHelper load
INFO: Get user by name: rsremote
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.helpers.UserHelper load
INFO: Get user by name: smrtpipe
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.helpers.UserHelper load
INFO: Get user by name: autodaemon
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save User: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save User: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save User: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save UserGroup: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save UserGroup: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.common.entities.EntityHelper save
INFO: Save UserGroup: 0
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.dbupdate.InitDbData addToUsers
INFO: Associated all (3) users with group all
Apr 12, 2013 9:05:31 AM com.pacbio.secondary.smrtportal.dbupdate.InitDbData addToJobs
INFO: Found 0 jobs associated with no groups
1745 [main] WARN org.hibernate.util.JDBCExceptionReporter - SQL Error: 1146, SQLState: 42S02
1745 [main] ERROR org.hibernate.util.JDBCExceptionReporter - Table 'smrtportal.InputGroup' doesn't exist
Exception in thread "main" javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: could not execute query
at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1235)
at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1168)
at org.hibernate.ejb.QueryImpl.getResultList(QueryImpl.java:250)
at com.pacbio.secondary.smrtportal.common.entities.EntityHelper.executeSelect(EntityHelper.java:407)
at com.pacbio.secondary.smrtportal.common.entities.EntityHelper.executeSelect(EntityHelper.java:415)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.addToInputs(InitDbData.java:155)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.<init>(InitDbData.java:74)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.main(InitDbData.java:362)
Caused by: org.hibernate.exception.SQLGrammarException: could not execute query
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:92)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at org.hibernate.loader.Loader.doList(Loader.java:2452)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2192)
at org.hibernate.loader.Loader.list(Loader.java:2187)
at org.hibernate.loader.custom.CustomLoader.list(CustomLoader.java:316)
at org.hibernate.impl.SessionImpl.listCustomQuery(SessionImpl.java:1832)
at org.hibernate.impl.AbstractSessionImpl.list(AbstractSessionImpl.java:165)
at org.hibernate.impl.SQLQueryImpl.list(SQLQueryImpl.java:179)
at org.hibernate.ejb.QueryImpl.getResultList(QueryImpl.java:241)
... 5 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'smrtportal.InputGroup' doesn't exist
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.Util.getInstance(Util.java:382)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1052)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3593)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3525)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1986)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2140)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2111)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2273)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1869)
at org.hibernate.loader.Loader.doQuery(Loader.java:718)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
at org.hibernate.loader.Loader.doList(Loader.java:2449)
... 12 more

**GenoMax** · 04-11-2013, 03:19 PM

You can also look at the logs to see if there are any additional hints in there:

common/log/smrtportal/*

Our efforts to make SMRTportal work on anything other than the narrowly supported OS's have been unsuccessful. Perhaps rhall may be able to help. You do have an error about groups in the log you posted.

**coldturkey** · 04-11-2013, 03:28 PM

Yeah I see that. I tried to import again and got the following log error

Apr 12, 2013 9:25:33 AM com.pacbio.secondary.smrtportal.common.helpers.InputHelper loadMetadata
INFO: Input not imported from metadata. It already exists. Path: /home/brian/Work_data/EC958_Genome_assembly/10kb_libs/B01_2
Apr 12, 2013 9:25:33 AM com.pacbio.secondary.smrtportal.common.helpers.InputDataHelper getFirstMetadataFile
INFO: Parse movie metadata collection path: /home/brian/Work_data/EC958_Genome_assembly/10kb_libs/B01_1
Apr 12, 2013 9:25:33 AM com.pacbio.secondary.smrtportal.common.helpers.InputHelper loadMetadata
INFO: Input not imported from metadata. It already exists. Path: /home/brian/Work_data/EC958_Genome_assembly/10kb_libs/B01_1
Apr 12, 2013 9:25:33 AM com.pacbio.secondary.smrtportal.common.helpers.InputDataHelper getFirstMetadataFile
INFO: Parse movie metadata collection path: /home/brian/Work_data/EC958_Genome_assembly/10kb_libs/B01_3
Apr 12, 2013 9:25:33 AM com.pacbio.secondary.smrtportal.common.helpers.InputHelper loadMetadata
INFO: Input not imported from metadata. It already exists. Path: /home/brian/Work_data/EC958_Genome_assembly/10kb_libs/B01_3

**rhall** · 04-11-2013, 03:31 PM

While it is not impossible to get SMRT Analysis running on 12.04, it is not straight forward.
Looks like a database issue, assuming it is not related to the new version of mysql in 12.04 you can try.

Code:

cd $SEYMOUR_HOME/etc/scripts
./drop_db.sh
./create_db.sh SMRTPortalSchema.sql
./dbdata.sh

Note only try this on a new install in which you do not care about the data in the db.

**coldturkey** · 04-11-2013, 03:36 PM

Hi rhall

I get an error in the last bit

./dbdata.sh [ 9:34AM]
./dbdata.sh: 15: /opt/smrtanalysis/etc/setup.sh: Syntax error: "(" unexpected

**rhall** · 04-11-2013, 03:40 PM

sorry

Code:

bash ./dbdata.sh

**coldturkey** · 04-11-2013, 03:48 PM

k that seemed to work and I have been able to import the lamdba test cell

**coldturkey** · 04-11-2013, 03:51 PM

I can also import my own data and so I seem to be over that hurdle. Hopefully it will be clear sailing from her on in. Thank you rhall and Genomax.

**GenoMax** · 04-11-2013, 03:52 PM

Great. That is half the battle .. now on to the rest.

@rhall: Does coldturkey need to fix the LANG variable you had previously posted in a different thread?

< LANG=en_US.UTF-8
< LC_ALL=en_US.UTF-8
< export LANG LC_ALL

**rhall** · 04-11-2013, 03:59 PM

Possibly if the machine is not set to a US locale. Although the only time I have seen the issue is when the locale has a very different time and data format, I believe english language versions of Ubuntu should not have a problem.
But yes the above three lines can be added to $SEYMOUR_HOME/analysis/etc/setup.sh to overcome the locale issue.

**coldturkey** · 04-11-2013, 04:08 PM

are there anymore changes that i should make?

**rhall** · 04-11-2013, 04:11 PM

Nothing obvious.
Try analyzing something and let us know how you get along.

**coldturkey** · 04-11-2013, 04:15 PM

Will do. Thank you both. Enjoy the weekend.

**coldturkey** · 04-14-2013, 08:50 PM

It seems that over the weekend smrtportal has decided it will not work. I now have no access to the webserver. I have tried turning on and off tomcat and I have rerun the configuration script several times. Nothing works

When I run ./smrtanalysis-1.4.0/etc/scripts/postinstall/test_smrtanalysis.sh I get
[localhost] Executing task 'apps'
[INFO]Mon, 15 Apr 2013 14:37:13 - Initiating apps sanity tests
[INFO]Mon, 15 Apr 2013 14:37:13 - ------- Testing the autodaemon -------
[INFO]Mon, 15 Apr 2013 14:37:13 - kodosd is running.
[INFO]Mon, 15 Apr 2013 14:37:13 - ------- Testing SMRTPortal web services -------
[INFO]Mon, 15 Apr 2013 14:37:13 - Testing http://localhost:8080/smrtportal/api
[INFO]Mon, 15 Apr 2013 14:37:13 - Failed portal sanity tests: Error - SMRTPortal web services are not accessible

Have you encountered this? Nothing has changed since I last ran the smrtportal on Friday

regards

Brian

**GenoMax** · 04-15-2013, 03:27 AM

We have never had any issues with SMRTportal once it gets installed and going.

It is obvious but have you tried to give the machine a reboot (if possible)?

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