{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/880","repository_url":"https://api.github.com/repos/broadinstitute/cromwell","labels_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/880/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/880/comments","events_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/880/events","html_url":"https://github.com/broadinstitute/cromwell/issues/880","id":156569482,"number":880,"title":"Cromwell restart MySQL Constraint Violation Duplicate Entry","user":{"login":"jsotobroad","id":13023616,"avatar_url":"https://avatars.githubusercontent.com/u/13023616?v=3","gravatar_id":"","url":"https://api.github.com/users/jsotobroad","html_url":"https://github.com/jsotobroad","followers_url":"https://api.github.com/users/jsotobroad/followers","following_url":"https://api.github.com/users/jsotobroad/following{/other_user}","gists_url":"https://api.github.com/users/jsotobroad/gists{/gist_id}","starred_url":"https://api.github.com/users/jsotobroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsotobroad/subscriptions","organizations_url":"https://api.github.com/users/jsotobroad/orgs","repos_url":"https://api.github.com/users/jsotobroad/repos","events_url":"https://api.github.com/users/jsotobroad/events{/privacy}","received_events_url":"https://api.github.com/users/jsotobroad/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/cromwell/labels/GreenFriends","name":"GreenFriends","color":"00FF00"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-05-24T17:52:17Z","updated_at":"2016-10-17T18:56:31Z","closed_at":"2016-10-17T18:56:31Z","body":"This task failed after a restart of Cromwell with the following stack trace.  We have seen similar errors before - #588.  This was only after one restart though.\r\n```\r\n2016-05-24 16:59:43,266 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(fd62961b):ApplyBQSR:11]: Starting call with pre-emptible VM\r\n\r\n2016-05-24 16:59:43,431 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(fd62961b)]: persisting status of ApplyBQSR:11 to Running.\r\n\r\n2016-05-24 16:59:43,526 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(fd62961b):ApplyBQSR:11]: Status change from - to Success\r\n\r\n2016-05-24 16:59:44,173 cromwell-system-akka.actor.default-dispatcher-13 ERROR - WorkflowActor [UUID(fd62961b)]: Completion work failed for call ApplyBQSR:11.\r\ncom.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '741-PairedEndSingleSampleWorkflow.ApplyBQSR-recalibrated_bam-11-' for key 'UK_SYM_WORKFLOW_EXECUTION_ID_SCOPE_NAME_ITERATION_IO'\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_72]\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_72]\r\n\tat sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_72]\r\n\tat java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_72]\r\n\tat com.mysql.jdbc.Util.handleNewInstance(Util.java:400) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.Util.getInstance(Util.java:383) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.SQLError.createSQLException(SQLError.java:973) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3847) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3783) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2447) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2594) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2545) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1901) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2113) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2049) ~[cromwell.jar:0.19]\r\n\tat com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2034) ~[cromwell.jar:0.19]\r\n\tat com.zaxxer.hikari.proxy.PreparedStatementProxy.executeUpdate(PreparedStatementProxy.java:61) ~[cromwell.jar:0.19]\r\n\tat com.zaxxer.hikari.proxy.PreparedStatementJavassistProxy.executeUpdate(PreparedStatementJavassistProxy.java) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$anonfun$run$8$$anonfun$apply$1.apply(JdbcActionComponent.scala:520) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$anonfun$run$8$$anonfun$apply$1.apply(JdbcActionComponent.scala:517) ~[cromwell.jar:0.19]\r\n\tat slick.jdbc.JdbcBackend$SessionDef$class.withPreparedInsertStatement(JdbcBackend.scala:354) ~[cromwell.jar:0.19]\r\n\tat slick.jdbc.JdbcBackend$BaseSession.withPreparedInsertStatement(JdbcBackend.scala:407) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$ReturningInsertActionComposerImpl.preparedInsert(JdbcActionComponent.scala:636) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$anonfun$run$8.apply(JdbcActionComponent.scala:517) ~[cromwell.jar:0.19]\r\n\tat scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245) ~[cromwell.jar:0.19]\r\n\tat scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245) ~[cromwell.jar:0.19]\r\n\tat scala.collection.immutable.List.foreach(List.scala:381) ~[cromwell.jar:0.19]\r\n\tat scala.collection.TraversableLike$class.map(TraversableLike.scala:245) ~[cromwell.jar:0.19]\r\n\tat scala.collection.immutable.List.map(List.scala:285) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run(JdbcActionComponent.scala:522) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$SimpleJdbcDriverAction.run(JdbcActionComponent.scala:32) ~[cromwell.jar:0.19]\r\n\tat slick.driver.JdbcActionComponent$SimpleJdbcDriverAction.run(JdbcActionComponent.scala:29) ~[cromwell.jar:0.19]\r\n\tat slick.backend.DatabaseComponent$DatabaseDef$$anon$2.liftedTree1$1(DatabaseComponent.scala:237) ~[cromwell.jar:0.19]\r\n\tat slick.backend.DatabaseComponent$DatabaseDef$$anon$2.run(DatabaseComponent.scala:237) ~[cromwell.jar:0.19]\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[na:1.8.0_72]\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_72]\r\n\tat java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_72]\r\n2016-05-24 16:59:44,174 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JesBackend [UUID(fd62961b):ApplyBQSRToUnmappedReads]: Starting call with pre-emptible VM\r\n2016-05-24 16:59:44,175 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(fd62961b)]: persisting status of ApplyBQSR:11 to Failed.\r\n2016-05-24 16:59:44,180 cromwell-system-akka.actor.default-dispatcher-13 ERROR - WorkflowActor [UUID(fd62961b)]: Duplicate entry '741-PairedEndSingleSampleWorkflow.ApplyBQSR-recalibrated_bam-11-' for key 'UK_SYM_WORKFLOW_EXECUTION_ID_SCOPE_NAME_ITERATION_IO'\r\n\r\n2016-05-24 16:59:44,175 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(fd62961b)]: persisting status of ApplyBQSR:11 to Failed.\r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/broadinstitute/cromwell/issues/comments/254299664","html_url":"https://github.com/broadinstitute/cromwell/issues/880#issuecomment-254299664","issue_url":"https://api.github.com/repos/broadinstitute/cromwell/issues/880","id":254299664,"user":{"login":"cjllanwarne","id":13006282,"avatar_url":"https://avatars.githubusercontent.com/u/13006282?v=3","gravatar_id":"","url":"https://api.github.com/users/cjllanwarne","html_url":"https://github.com/cjllanwarne","followers_url":"https://api.github.com/users/cjllanwarne/followers","following_url":"https://api.github.com/users/cjllanwarne/following{/other_user}","gists_url":"https://api.github.com/users/cjllanwarne/gists{/gist_id}","starred_url":"https://api.github.com/users/cjllanwarne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjllanwarne/subscriptions","organizations_url":"https://api.github.com/users/cjllanwarne/orgs","repos_url":"https://api.github.com/users/cjllanwarne/repos","events_url":"https://api.github.com/users/cjllanwarne/events{/privacy}","received_events_url":"https://api.github.com/users/cjllanwarne/received_events","type":"User","site_admin":false},"created_at":"2016-10-17T18:56:31Z","updated_at":"2016-10-17T18:56:31Z","body":"This particular problem cannot happen with the new database layout in 21+.\r\n\r\nWe may have other problems, but this one is done."}}
{"actor":{"display_login":"cjllanwarne"}}