Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

What causes GATK "Unable to retrieve result"?

INFO 13:25:37,379 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:25:37,379 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-30-gf2ef8d1, Compiled 2012/02/17 20:18:04
INFO 13:25:37,379 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:25:37,379 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 13:25:37,379 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 13:25:37,379 HelpFormatter - Program Args: -T UnifiedGenotyper -l INFO -glm BOTH -et NO_ET -stand_call_conf 30 -stand_emit_conf 10 -R C:\Illumina\MiSeq Reporter\Genomes\HIV1_HXB2\Sequence\WholeGenomeFASTA\HXB2K03455.fa -nt 8 -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\KERM00_S1.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\KERM12_S2.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\MRTJ0_S3.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\MRTM06_S4.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\MRTM18_S5.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\XYQUJ0_S6.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\XYQUM36_S7.bam -I D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\XYQUM60_S8.bam -o D:\Illumina\MiSeqAnalysis\121219_M01400_0003_000000000-A16J4\Data\Intensities\BaseCalls\Alignment3\variants_G1.1.vcf
INFO 13:25:37,379 HelpFormatter - Date/Time: 2012/12/21 13:25:37
INFO 13:25:37,379 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:25:37,379 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:25:37,410 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:25:38,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:25:38,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
INFO 13:25:38,486 MicroScheduler - Running the GATK in parallel mode with 8 concurrent threads

Below are error messages from GATK.

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to retrieve result
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:137)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
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:90)
Caused by: java.util.concurrent.ExecutionException: org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error has occurred during traversal
at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
at java.util.concurrent.FutureTask.get(Unknown Source)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:130)
... 5 more
Caused by: org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error has occurred during traversal
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:88)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ArithmeticException: / by zero
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:195)
at org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:171)
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.initializeReferenceSequence(LocusReferenceView.java:153)
at org.broadinstitute.sting.gatk.datasources.providers.LocusReferenceView.(LocusReferenceView.java:101)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:47)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:72)
... 5 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.4-30-gf2ef8d1):
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: Unable to retrieve result
ERROR ------------------------------------------------------------------------------------------

Answers

Sign In or Register to comment.