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RUNTIME ERROR(version 1.5-16-g58245bf) - MESSAGE:An error occurred during the traversal.

jmartinjmartin Member Posts: 1

I'm running the UnifiedGenotyper on a large number of metagenomic samples (~110) that have been mapped by BWA against a database of 671 reference genomes. I know that the UG is meant only for diploid use, but I was hoping to use the vcf output to get at base frequencies at specific loci (as opposed to the probability of whatever diploid genotype is predicted).

I'm running the UG with a 63Gb memory allocation, using 12 threads. Here is the error message I received:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error occurred during the traversal.
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.getTraversalError(HierarchicalMicroScheduler.java:356)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.regex.Pattern$Start.(Pattern.java:3043)
at java.util.regex.Pattern.compile(Pattern.java:1480)
at java.util.regex.Pattern.(Pattern.java:1133)
at java.util.regex.Pattern.compile(Pattern.java:823)
at java.lang.String.split(String.java:2292)
at net.sf.samtools.SAMTextHeaderCodec$ParsedHeaderLine.(SAMTextHeaderCodec.java:272)
at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:80)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:391)
at net.sf.samtools.BAMFileReader.(BAMFileReader.java:144)
at net.sf.samtools.BAMFileReader.(BAMFileReader.java:114)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:514)
at net.sf.samtools.SAMFileReader.(SAMFileReader.java:167)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReaderInitializer.call(SAMDataSource.java:933)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMReaders.(SAMDataSource.java:794)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.createNewResource(SAMDataSource.java:753)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.getAvailableReaders(SAMDataSource.java:724)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.seek(SAMDataSource.java:525)
at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(MicroScheduler.java:175)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:65)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.5-16-g58245bf):
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

I'm worried that this error might be caused by my use of the UG for such a non-traditional experiment (100+ metagenomic samples mapped to 671 reference genomes), but I wanted to check here to see if maybe it was a more mundane bug, and the UG should otherwise be working for my input (albeit with the genotypes & probabilities called under the false assumption that my data is diploid ... all I want is the base frequencies at snp loci)

ERROR
ERROR MESSAGE: An error occurred during the traversal.
ERROR -----------------------------------------------------------------------------------------

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin
    Accepted Answer

    Hi there,

    For what you're trying to do, you should really upgrade to the latest version of GATK. We are currently on v 2.2-5. Please join us in the future...

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin
    Accepted Answer

    Hi there,

    For what you're trying to do, you should really upgrade to the latest version of GATK. We are currently on v 2.2-5. Please join us in the future...

    Geraldine Van der Auwera, PhD

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