Hi Ni,
my apologies that I have not been able to look at this. I am tracking this
as an issue on our Picard github issues site:
https://github.com/broadinstitute/picard/issues/72
N
On Fri, Sep 5, 2014 at 2:32 PM, Nils Homer <nho...@broadinstitute.org>
wrote:
> 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 <nihu...@genetics.wustl.edu>
> 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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