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Error running Cromwell 27-SNAP (build from master)

kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

I just started a Cromwell server running against a database used with Cromwell 25 and upon startup, I get the following errors:

[ERROR] [04/19/2017 18:14:32.636] [cromwell-system-akka.actor.default-dispatcher-4] [akka://cromwell-system/user/cromwell-service/ServiceRegistryActor/MetadataService] Error summarizing metadata
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '"SUMMARY_STATUS_ENTRY" where ("SUMMARY_TABLE_NAME" = 'WORKFLOW_METADATA_SUMMARY_' at line 1

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Have you tried turning it off and on again?

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    repeatedly ;)@ChrisL knows the answer

  • alphahmedalphahmed JAPANMember

    Using Cromwell 29, just for a basic regular GATK workflow, I keep getting very similar error at the recalibration step ("BaseRecalibrator" walker of GATK 3.8).

    [2017-11-27 16:44:21,60] [error] Failed to summarize metadata
    java.sql.SQLTransientConnectionException: db - Connection is not available, request timed out after 8544ms.
    at com.zaxxer.hikari.pool.HikariPool.createTimeoutException(HikariPool.java:548)
    at com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:186)
    at com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:145)
    at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:83)
    at slick.jdbc.hikaricp.HikariCPJdbcDataSource.createConnection(HikariCPJdbcDataSource.scala:18)
    at slick.jdbc.JdbcBackend$BaseSession.(JdbcBackend.scala:439)
    at slick.jdbc.JdbcBackend$DatabaseDef.createSession(JdbcBackend.scala:47)
    at slick.jdbc.JdbcBackend$DatabaseDef.createSession(JdbcBackend.scala:38)
    at slick.basic.BasicBackend$DatabaseDef.acquireSession(BasicBackend.scala:218)
    at slick.basic.BasicBackend$DatabaseDef.acquireSession$(BasicBackend.scala:217)
    at slick.jdbc.JdbcBackend$DatabaseDef.acquireSession(JdbcBackend.scala:38)
    at slick.basic.BasicBackend$DatabaseDef$$anon$2.run(BasicBackend.scala:239)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

    The only linked database to this run is the "knownSites" vcf file, which seems to be already loaded into the inputs directory of cromwell-excusions for each sample.

  • EADGEADG KielMember ✭✭✭

    Hi @alphahmed .

    the database which is meant in your error is the database from cromwell, running on default options, cromwell creates an in-memory database. Did you try to run cromwell with a decided database?

    The second, did you check the load on your server? I get a similar error when the server runs on extremely high loads and the DB is to slow to answer at an adequate amount of time.

    Greetings EADG

  • alphahmedalphahmed JAPANMember

    Thanks EADG!
    No I didn't assign a database to cromwell upon running it.
    You're explanation on the second one makes a lot of sense, I am applying an extreme load on the server, which is very likely the cause of both errors.

    I appreciate it!

  • ChrisLChrisL Cambridge, MAMember, Broadie, Dev admin

    Just a side note on this, for whatever reason the default in-memory database seems to scale significantly worse than a regular MySQL instance, so don't give up hope until you've tried the same scale test backed by a MySQL DB!

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