htsjdk.samtools.SAMException: Query asks for data past end of contig at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181) at picard.analysis.directed.TargetMetricsCollector.<init>(TargetMetricsCollector.java:225) at picard.analysis.directed.HsMetricCollector.<init>(HsMetricCollector.java:47) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:96) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:48) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:108) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)

sourceforge.net | 4 months ago
  1. 0

    SAM tools / Mailing Lists

    ehc.ac | 1 year ago
    htsjdk.samtools.SAMException: Query asks for data past end of contig at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181) at picard.analysis.directed.TargetMetricsCollector.<init>(TargetMetricsCollector.java:225) at picard.analysis.directed.HsMetricCollector.<init>(HsMetricCollector.java:47) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:96) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:48) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:108) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
  2. 0

    SAM tools / Mailing Lists

    sourceforge.net | 4 months ago
    htsjdk.samtools.SAMException: Query asks for data past end of contig at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181) at picard.analysis.directed.TargetMetricsCollector.<init>(TargetMetricsCollector.java:225) at picard.analysis.directed.HsMetricCollector.<init>(HsMetricCollector.java:47) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:96) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:48) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:108) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
  3. 0

    SAM tools / Mailing Lists

    sourceforge.net | 7 months ago
    htsjdk.samtools.SAMException: Exception closing FileOutputStream for /data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.2781500592681706581.t mp/29668.tmp at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:74) at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:49) at htsjdk.samtools.util.ResourceLimitedMap$1.removeEldestEntry(ResourceLimitedMap.java:59)
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  5. 0

    Tophat v2.1.1 reports identical alignments and does not mark either as secondary.

    GitHub | 7 months ago | MatthewRalston
    htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 96: null:NB501257:32:HWCMVBGXX:1:21209:24100:6206
  6. 0

    SAM tools / Mailing Lists

    sourceforge.net | 1 year ago
    htsjdk.samtools.SAMException: Exception closing FileOutputStream for /data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.5751822609546779855.t mp/27421.tmp at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:74) at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:49) at htsjdk.samtools.util.ResourceLimitedMap$1.removeEldestEntry(ResourceLimitedMap.java:59)

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    Root Cause Analysis

    1. htsjdk.samtools.SAMException

      Query asks for data past end of contig at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181) at picard.analysis.directed.TargetMetricsCollector.<init>(TargetMetricsCollector.java:225) at picard.analysis.directed.HsMetricCollector.<init>(HsMetricCollector.java:47) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:96) at picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:48) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:108) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)

      at picard.cmdline.PicardCommandLine.instanceMain()
    2. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
      2. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
      2 frames