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)