htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 5

broadinstitute.org | 3 months ago
  1. 0

    (How to) Map and clean up short read sequence data efficiently — GATK-Forum

    broadinstitute.org | 3 months ago
    htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 5
  2. 0

    GitHub comment 634#241115911

    GitHub | 4 months ago | yfarjoun
    htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 8
  3. 0

    Exception running MergeBamAlignment after #622

    GitHub | 4 months ago | tfenne
    htsjdk.samtools.SAMException: Requesting earlier reference sequence: 0 < 8
  4. Speed up your debug routine!

    Automated exception search integrated into your IDE

  5. 0

    Error for Picard CollectInsertSizeMetrics

    GitHub | 1 month ago | raphenya
    htsjdk.samtools.SAMException: Reference sequence (424) not found in ../../galaxy/tool-data/grch38/seq/grch38.fa
  6. 0

    Multiple reads with same name

    GitHub | 4 months ago | Phillip-a-richmond
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 2: 17-126946-I:17-126946-I-:::::::::::2548929:0

    Not finding the right solution?
    Take a tour to get the most out of Samebug.

    Tired of useless tips?

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. htsjdk.samtools.SAMException

      Requesting earlier reference sequence: 0 < 5

      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:622)
      3. picard.sam.AbstractAlignmentMerger.transferAlignmentInfoToPairedRead(AbstractAlignmentMerger.java:580)
      4. picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:390)
      5. picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:157)
      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