Breakdancer Output in multisample problem

[kinu]

Hi everyone,
I have 4 samples (matepair illumina) and run Breakdancer_max as follows:
bam2cfg.pl -h -g -q 10 sample1.bam sample2.bam sample3.bam sample4.bam >sample1_2_sample3_4.cfg
it worked without error msg.
breakdancer-max -o chrX -q 10 -d Fastq_SVReadsFile_X -g GBrowse_OUTFile_X.bed -l -h sample1_2_sample3_4.cfg >chrX_SV_allSample.ctx
This also worked generating outputs with last mag as Kahan error (which i ignored as read on other blogs https://www.biostars.org/p/97367/#98866)
The problem is that the output file chrX_SV_allSample.ctx only contains SV specific to sample4. while all other samples contains NA in their columns. I donot know where i am making mistake.
e.g.
Software: 1.4.4-unstable-7-6213d5a (commit 6213d5a)
Command: breakdancer-max -o chrX -q 10 -d Fastq_SVReadsFile_X -g GBrowse_OUTFile_X.bed -l -h sample1_2_sample3_4.cfg
Library Statistics:
sample4.bam mean:4218.95 std:552.31 uppercutoff:6393.21 lowercutoff:1975.9 readlen:50.82 library:tight reflen:111700677 seqcov:0.939753 phycov:39.008 1:8326 2:6802 3:2818 4:436 8:8414 32:20695
sample4.bam mean:3889.35 std:680.67 uppercutoff:6865.34 lowercutoff:1401.76 readlen:50.82 library:wide reflen:111700677 seqcov:0.701866 phycov:26.8576 1:6586 2:2710 3:2022 4:326 8:6506 32:15637
Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Allele_frequency sample1.bam sample2.bam sample3.bam sample4.bam
chrX 229 312+317- chrX 292963 312+317- INV 6106 99 118 sample4.bam|118 -nan NA NA NA NA
chrX 327014 58+52- chrX 372108 58+52- INV -1620 70 20 sample4.bam|20 -nan NA NA NA NA
chrX 372154 58+52- chrX 430662 103+43- INV 10905 99 43 sample4.bam|43 0.301335 NA NA NA 1.40
chrX 491312 5+2- chrX 494412 5+2- INV -3118 34 2 sample4.bam|2 -nan NA NA NA NA
Please guide.
Any help or suggestion is valuable

[ernfrid]

Do your BAM files have proper readgroup information in the header and in the reads? Can you post your configuration file?