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I get this error from a MarkDuplicates and all the questions I've found online comment on merging fastq file and ending up with read name from more than one original fastq files. I get this error without having merged fastq files and only having one pair of reads in bam file with same name with flags 129 and 81 (so read 2 and read 1). Is there any other reason why this message could come up?
I'm using an older version of the Picard (as a part of pipeline) though so if there has been bugs in this area then I'm likely hitting them.