breakdancer bam2cfg error

[mei404]

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!

[Robby]

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

[Robby]

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

[cmonat]

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.