BQSRGatherer exception
Posted in Ask the GATK team | Last updated on


Comments (27)

When using queue for BQSR scatter/gather parellelism I've been seeing the following:

java.lang.IllegalArgumentException: Table1 188,3 not equal to 189,3
        at org.broadinstitute.sting.utils.recalibration.RecalUtils.combineTables(RecalUtils.java:808)
        at org.broadinstitute.sting.utils.recalibration.RecalibrationReport.combine(RecalibrationReport.java:147)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BQSRGatherer.gather(BQSRGatherer.java:86)
        at org.broadinstitute.sting.queue.function.scattergather.GathererFunction.run(GathererFunction.scala:42)
        at org.broadinstitute.sting.queue.engine.InProcessRunner.start(InProcessRunner.scala:53)
        at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:434)
        at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:156)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:171)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

I'm using gatk version: v2.4-7-g5e89f01 (I can't keep up the pace with you guys). I'm wondering if this is a know issue, and if so, if there is a workaround or a fix in later GATK versions.

Cheers, Johan


Return to top Comment on this article in the forum