picard markdup error:Value was put into PairInfoMap more than once
I get the error information Value was put into PairInfoMap more than once when I use picard to mark duplication.
I have already tested the newest version bwa 0.7.16a and picard 2.10.7.
My mapping paramater is bwa mem -M.
All paired reads id are unique in fq.
I use samtools view this.bam|grep readsname, the output is captured as this picture:
I have read the pages about this trouble asked before on gatk forum and biostar forum. I think the secondary hits in bam are correct, compared to the previous reported condition, but not for sure. Therefore, I come here to ask for professional help.