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I don't understand the error message of picard tools markduplicates
Hello, I started to work with Nextseq500 data for variant calling. At the moment each job will terminate with the following error message:
INFO 2016-06-24 12:18:47 MarkDuplicates Tracking 1032268 as yet unmatched pairs. 6094 records in RAM.
INFO 2016-06-24 12:18:52 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 5s. Last read position:
INFO 2016-06-24 12:18:52 MarkDuplicates Tracking 1040251 as yet unmatched pairs. 2676 records in RAM.
[Fri Jun 24 12:19:17 CEST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 14.90 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 10:
When I repeated the job, Picard tools crahed already after 40,000,000 records. There is enough disk space. Jobs were running on a Linux machine with 40 cores and 512GB ram. When I looked for the error message in WWW I always found a read name after "Value was put into PairInfoMap more than once. 10:". Here a read name is missing. What does "10:" mean? I used the following softwares: bwa-0.7.13, samtools-1.3.1, Picard Tools several versions 1.139-2.4.1. Could this be a data or an envrionmental problem?