[svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position...

[John B. <jo...@we...>]

Hi there,

We're trying to use svtoolkit for SV  detection on some deep-sequencing data.  This 
particular project comprises data from many (up to 800) BAMs.  I've reduced the number to 
80 and I still see this kind of error.  Where might it come from and how might I fix it?

I'm not sure which part of the log is most useful, but I've appended what looks to be most 
informative.

Thanks,
John Broxholme
WTCHG,
Oxford, UK

...
INFO  00:19:23,590 SVDiscovery - Clustering: LR split size 14 / 95 maximal clique size 2 
clique count 3
INFO  00:19:23,590 SVDiscovery - Clustering: LR split size 12 / 95 maximal clique size 1 
clique count 18
INFO  00:19:23,590 SVDiscovery - Processing cluster 14:24437577-24437715 
14:24519740-24520124 LR 10
INFO  00:19:24,712 SVDiscovery - Processing cluster 14:24425879-24426190 
14:24461366-24461735 LR 6
Error: Exception processing cluster: Permitted to write any record upstream of position 
24427689, but a record at 14:24426202 was just added.
Cluster: 14:24425879-24426190 14:24461366-24461735 LR 6
[GC 2440851K->2036038K(2645952K), 0.0058190 secs]
[Full GC 2036038K->34379K(2645952K), 0.7118760 secs]
##### ERROR 
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.IllegalArgumentException: Permitted to write any record upstream of position 
24427689, but a record at 14:24426202 was just added.
         at 
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.noteCurrentRecord(SortingVCFWriterBase.java:101)
         at 
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter.noteCurrentRecord(SortingVCFWriter.java:55)
         at 
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.add(SortingVCFWriterBase.java:123)
         at 
org.broadinstitute.sv.util.vcf.VCFWriterFactory$VCFWriterAdapter.add(VCFWriterFactory.java:76)
         at 
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:641)
         at 
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:439)
         at 
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:337)
         at 
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:186)
         at 
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:166)
         at 
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45)
         at 
org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
         at 
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76)
         at 
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
         at 
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
         at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105)
         at 
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
         at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67)
         at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR 
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions 
http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Permitted to write any record upstream of position 24427689, but a 
record at 14:24426202 was just added.
##### ERROR 
------------------------------------------------------------------------------------------
         at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
         at 
org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
         at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
         at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
         at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
         at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
         at 
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
         at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
         at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
INFO  00:19:40,719 QGraph - 74 Pend, 2 Run, 0 Fail, 12 Done
...