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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.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

ReduceReads Unknown Contig

kylechbkylechb Boston Children's HospitalMember


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(
at org.broadinstitute.sting.utils.MRUCachingSAMSequenceDictionary.getSequence(
at org.broadinstitute.sting.utils.GenomeLocParser.validateGenomeLoc(
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(
at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(
at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView.getReferenceContext(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.aggregateMapData(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(


Best Answer


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