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  • breakdancer bam2cfg error

    when i run perl /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl ./test_sort.bam , this two error,
    Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 71, <BAM> line 26.
    Use of uninitialized value in hash element at /usr/local/src/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl line 173.
    who know how to solve?
    I feel anxious! thanks!

  • #2
    I assume, that your bam file has no read group in the header. Could you run samtools view -H file.bam and post the result, please?

    Best regards
    Robby

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    • #3
      But I have an error message as well:

      $recordcounter > $expected_max: 30001 > 30000

      $recordcounter counts the number of reads in the bam-file.
      $expected_max = 3*($#libas+1)*$opts{n}.
      $opts{n} is the number of observation required to estimate mean and s.d. insert size (default: 10000)
      $#libas is in my case 0, but I am not sure about the meaning

      Does somebody understand the error message or knows how to solve the problem?

      Thanks

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      • #4
        Hi,

        since the time of theses messages did you solve this problem ? because I have exactly the same, but my BAMs files have an RG so ... Any idea?
        Thank you!

        C.

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