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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
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ReduceReads Unknown Contig

kylechbkylechb Boston Children's HospitalMember

Hello,

I am new to the field, so please forgive me if this has a simple answer. I am attempting to call variants on 6 whole exome sequences. The best practices documentation suggested using 30 or more samples, so I downloaded 24 bam files from the 1000genomes database to use with mine. However, whenever I attempted to use ReduceReads on the files, I received the following error right near 100% completion:

ERROR MESSAGE: BUG: requested unknown contig=NC_007605 index=-1

I am using the latest b37 reference file from the bundle, and I have tried re-indexing it and re-forming the .dict file. Here is the stack trace from the above error. What is causing this, and how do I fix it?

ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: BUG: requested unknown contig=NC_007605 index=-1
at org.broadinstitute.sting.utils.MRUCachingSAMSequenceDictionary.updateCache(MRUCachingSAMSequenceDictionary.java:178)
at org.broadinstitute.sting.utils.MRUCachingSAMSequenceDictionary.getSequence(MRUCachingSAMSequenceDictionary.java:109)
at org.broadinstitute.sting.utils.GenomeLocParser.validateGenomeLoc(GenomeLocParser.java:284)
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:239)
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:449)
at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView.getReferenceContext(ReadReferenceView.java:98)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:139)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:128)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.aggregateMapData(TraverseReadsNano.java:119)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:101)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

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