java.lang.IllegalArgumentException: Invalid fastq character:

biostars.org | 6 months ago
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    SAM file wrong? help with validatesamfile

    biostars.org | 6 months ago
    java.lang.IllegalArgumentException: Invalid fastq character:

    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Invalid fastq character:

      at htsjdk.samtools.SAMUtils.fastqToPhred()
    2. HTS JDK
      SamFileValidator.validateSamFileSummary
      1. htsjdk.samtools.SAMUtils.fastqToPhred(SAMUtils.java:407)
      2. htsjdk.samtools.SAMUtils.fastqToPhred(SAMUtils.java:385)
      3. htsjdk.samtools.SAMRecord.setBaseQualityString(SAMRecord.java:277)
      4. htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:326)
      5. htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248)
      6. htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236)
      7. htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212)
      8. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545)
      9. htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:519)
      10. htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:269)
      11. htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:200)
      12. htsjdk.samtools.SamFileValidator.validateSamFileSummary(SamFileValidator.java:128)
      12 frames
    3. picard.sam
      ValidateSamFile.doWork
      1. picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:187)
      1 frame
    4. picard.cmdline
      PicardCommandLine.main
      1. picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
      2. picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
      3. picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
      3 frames