htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 8

GitHub | tfenne | 7 months ago
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    GitHub | 7 months ago | yfarjoun
    htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 8
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    GitHub | 7 months ago | tfenne
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    htsjdk.samtools.SAMException: Reference sequence (424) not found in ../../galaxy/tool-data/grch38/seq/grch38.fa

    Root Cause Analysis

    1. htsjdk.samtools.SAMException

      Requesting earlier reference sequence: 0 < 8

      at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get()
    2. HTS JDK
      ReferenceSequenceFileWalker.get
      1. htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:82)
      1 frame
    3. picard.sam
      MergeBamAlignment.doWork
      1. picard.sam.AbstractAlignmentMerger.calculateMdAndNmTags(AbstractAlignmentMerger.java:596)
      2. picard.sam.AbstractAlignmentMerger.clipForOverlappingReads(AbstractAlignmentMerger.java:628)
      3. picard.sam.AbstractAlignmentMerger.transferAlignmentInfoToPairedRead(AbstractAlignmentMerger.java:580)
      4. picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:390)
      5. picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:152)
      6. picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:266)
      6 frames
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames