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  • aquleaf
    Member
    • Mar 2010
    • 38
    #1

    Empty sequence dictionary

    Hi.

    When I used picardtools ValidateSamFile, it reported the empty sequence dictionary error in sam file. What does this error mean?

    Wish help! Thanks very much in advance!
    Tags: None
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544
    #2
    Are there no @SQ lines in the SAM header?

    Comment

    • DNASpeaks
      Junior Member
      • Oct 2012
      • 5
      #3
      trouble converting sam to bam, ValidateSamFile output "empty seq group"

      Originally posted by maubp View Post
      Are there no @SQ lines in the SAM header?
      Hello Everyone,
      I am having trouble converting the sam files to bam using samtools. I used this cmd to convert my sam to bam -

      samtools view -bT hg19.fa s_chip2.sam > s_chip2.bam
      I got this error.
      Parse error at line 7707082: sequence and quality are inconsistent
      Aborted


      I ran ValidateSamFile.jar, a picard tool and got the following error, hundreds of them -

      WARNING: Read name HWI-ST798R:82: D18MUACXX:2:1101:2025:1987, A record is missing a read group
      ERROR: Record 5, Read name HWI-ST798R:82: D18MUACXX:2:1101:8625:1992, Empty sequence dictionary.

      I am not sure how to fix this, any help is appreciated.

      Comment

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