Thanks Ni for the report, we will take a look at it over the next week.
Nils
On Fri, Sep 5, 2014 at 1:19 PM, Ni Huang <[email protected]> wrote:
> Hi,
>
> I am having the "Value was put into PairInfoMap more than once" error
> from MarkDuplicates, and it seems it's caused by chimeric
> reads/supplementary alignment produced by bwa mem:
>
> Error message:
> Exception in thread "main" htsjdk.samtools.SAMException: Value was put
> into PairInfoMap more than once. 3:
> 1:HW-ST997:617:HADL0ADXX:1:1114:15556:79712
>
> Reads causing problem:
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 161 chr10 124174955 0 45S56M
> chr13 91710177 0
> TATCTATATAAAAATACATACACAGACAGACAGACAGAAAGAGAGACAGACAGACAGACAGACAGACAGACAGACGGACGGACGGACGGACGGACGGACGG
> CCCFFFFFHHHHHJIJJJJJJJJJJJJJJJJJIIJJIIJJIIJIJJJJIIJJJJJIIJJIJJIIIIJHHFFHFFFDDDDBBDDDDBDDDDDDDDDDDDDDB
> NM:i:1 AS:i:51 XS:i:51 SA:Z:chr13,91710177,-,43S31M27S,0,0; MQ:i:0 RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 81 chr10 124174955 0 38S63M
> chr13 91710177 0
> ATAAAAATACATACACAGACAGACAGACAGAAAGAGAGACAGACAGACAGACAGACAGACAGACAGACGGACGGACGGACGGACGGACGGACGGACGGACG
> CDDEEDDDDDEEDDDDDDDDDDDDDDEDDDCDCDDECCEDEEFFFFFFFHHHHHHFJJIGIIJJJJJIGIGJJJIIJIFEGEHGJJJJGHHHHDDFFFCCC
> NM:i:3 AS:i:52 XS:i:51 SA:Z:chr13,91710177,+,50S31M20S,0,0; MQ:i:0 RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 2145 chr13 91710177 0 50H31M20H
> chr10 124174955 0 TCTGTCTGTCTGTCTCTCTTTCTGTCTGTCT
> HHFFFFFFFEEDECCEDDCDCDDDEDDDDDD NM:i:0 AS:i:31 XS:i:29
> SA:Z:chr10,124174955,-,38S63M,0,3; MQ:i:0 RG:Z:1
> HW-ST997:617:HADL0ADXX:1:1114:15556:79712 2193 chr13 91710177 0 43H31M27H
> chr10 124174955 0 TCTGTCTGTCTGTCTCTCTTTCTGTCTGTCT
> JIIJJJJJIIJJJJIJIIJJIIJJIIJJJJJ NM:i:0 AS:i:31 XS:i:29
> SA:Z:chr10,124174955,+,45S56M,0,1; MQ:i:0 RG:Z:1
>
> The version of picard I am using is version 1.119. I think picard started
> supporting the 0x800 flag/supplementary alignment since version 1.96, but
> perhaps not all modules handle those reads correctly?
>
> Is there a work-around of this issue at the moment?
>
> Many thanks,
> Ni
>
>
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