java.lang.IllegalArgumentException: Invalid fastq character: 

biostars.org | 4 months ago
  1. 0

    SAM file wrong? help with validatesamfile

    biostars.org | 4 months ago
    java.lang.IllegalArgumentException: Invalid fastq character: 
  2. 0
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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Invalid fastq character: 

      at htsjdk.samtools.SAMUtils.fastqToPhred()
    2. HTS JDK
      SamReader$AssertingIterator.next
      1. htsjdk.samtools.SAMUtils.fastqToPhred(SAMUtils.java:419)
      2. htsjdk.samtools.SAMUtils.fastqToPhred(SAMUtils.java:398)
      3. htsjdk.samtools.SAMRecord.setBaseQualityString(SAMRecord.java:258)
      4. htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:319)
      5. htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:247)
      6. htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:235)
      7. htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:211)
      8. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:514)
      9. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:488)
      9 frames
    3. picard.sam
      SortSam.doWork
      1. picard.sam.SortSam.doWork(SortSam.java:74)
      1 frame
    4. picard.cmdline
      CommandLineProgram.instanceMainWithExit
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
      2. picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:124)
      2 frames
    5. picard.sam
      SortSam.main
      1. picard.sam.SortSam.main(SortSam.java:61)
      1 frame