strange output of merged1.txt

[woodoo46]

Hi,

this may not be a bug, I may have used juicer.sh in a wrong way. I got the merged1.txt like this

0 ptg000001l 22025 0 0 ptg000001l 10968211 1
0 ptg000001l 22715 0 0 ptg000001l 18200059 1
0 ptg000001l 23038 0 0 ptg000001l 709230 1
0 ptg000001l 23434 0 0 ptg000001l 1077165 1
0 ptg000001l 23615 0 0 ptg000001l 11593927 1
0 ptg000001l 23566 0 0 ptg000001l 8866253 1
0 ptg000001l 23536 0 0 ptg000001l 13814162 1
0 ptg000001l 23503 0 0 ptg000001l 24037 1
0 ptg000001l 23796 0 0 ptg000001l 25009 1
0 ptg000001l 23668 0 0 ptg000001l 23841 1
0 ptg000001l 25098 0 0 ptg000001l 17698588 1

The bwa command in the merged_dedup.bam is like this:

bwa mem -K 320000000 -SP5M -t 20 -R @rg\tID:Sample_L002_001\tSM:HiC_sample\tPL:ILM\tLB:HiC_library references/contig.fasta /data/hi-c/analysis/juicer/splits/Sample_L002_R1_001.fastq.gz /data/hi-c/analysis/juicer/splits/Sample_L002_R2_001.fastq.gz

Is "sam_to_pre.awk" looking for some kind of tag "rc:"/ in the bam file?

Thanks!

George