Latest Release: 8/9/18
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Clone workspace - Error: Lock wait timeout exceeded; try restarting transaction

Hello, thank you for great tool. I would like to start using Firecloud with GATK4 pipeline. I got free credits, and I am now trying to start analysis with pre-processing workflow help-gatk/Pre-processing_b37_v3.

However, I am not able to clone it - I will get this error:

Error: Lock wait timeout exceeded; try restarting transaction

Code: 500
Occurred: January 23, 2018, 9:18 AM GMT+1
Source: rawls
Cause:
Message: Lock wait timeout exceeded; try restarting transaction
Source: rawls
Stack Trace:
at sun.reflect.NativeConstructorAccessorImpl.newInstance0 (NativeConstructorAccessorImpl.java:-2)
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 com.mysql.jdbc.Util.handleNewInstance (Util.java:425)
at com.mysql.jdbc.Util.getInstance (Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException (SQLError.java:951)
at com.mysql.jdbc.MysqlIO.checkErrorPacket (MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket (MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand (MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect (MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL (ConnectionImpl.java:2490)
at com.mysql.jdbc.PreparedStatement.executeInternal (PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal (PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal (PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate (PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeBatchedInserts (PreparedStatement.java:1548)
at com.mysql.jdbc.PreparedStatement.executeBatchInternal (PreparedStatement.java:1253)
at com.mysql.jdbc.StatementImpl.executeBatch (StatementImpl.java:970)
at com.zaxxer.hikari.proxy.StatementProxy.executeBatch (StatementProxy.java:116)
at com.zaxxer.hikari.proxy.PreparedStatementJavassistProxy.executeBatch (PreparedStatementJavassistProxy.java:-1)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$anonfun$run$9.apply (JdbcActionComponent.scala:529)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$anonfun$run$9.apply (JdbcActionComponent.scala:523)
at slick.jdbc.JdbcBackend$SessionDef$class.withPreparedStatement (JdbcBackend.scala:347)
at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement (JdbcBackend.scala:407)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl.preparedInsert (JdbcActionComponent.scala:498)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run (JdbcActionComponent.scala:523)
at slick.driver.JdbcActionComponent$SimpleJdbcDriverAction.run (JdbcActionComponent.scala:32)
at slick.driver.JdbcActionComponent$SimpleJdbcDriverAction.run (JdbcActionComponent.scala:29)
at slick.dbio.DBIOAction$$anon$1$$anonfun$run$1.apply (DBIOAction.scala:161)
at slick.dbio.DBIOAction$$anon$1$$anonfun$run$1.apply (DBIOAction.scala:161)
at scala.collection.Iterator$class.foreach (Iterator.scala:891)
at scala.collection.AbstractIterator.foreach (Iterator.scala:1334)
at scala.collection.IterableLike$class.foreach (IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach (Iterable.scala:54)
at slick.dbio.DBIOAction$$anon$1.run (DBIOAction.scala:161)
at slick.dbio.DBIOAction$$anon$1.run (DBIOAction.scala:158)
at slick.backend.DatabaseComponent$DatabaseDef$$anon$2.liftedTree1$1 (DatabaseComponent.scala:237)
at slick.backend.DatabaseComponent$DatabaseDef$$anon$2.run (DatabaseComponent.scala:237)
at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:624)
at java.lang.Thread.run (Thread.java:748)

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    Could you try cloning the workspace again? The error message you have there suggests retrying as a first step, as often it is transient. Sometimes there are little hiccups that result in issues like this, but if it persists, or if the issue comes up frequently, we do want to know so we can take a look.

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