No @RG in bam files, so Picard cannot MergeDuplicates

[markram4]

I am trying to run the methlypy paired-end-pipeline, but I'm getting an error when it is trying to merged PCR duplicates. It appears it is not atting read group IDs to the sam/bam file after mapping, so Picard cannot merge read groups.

Thanks!

Exception in thread "main" java.lang.NullPointerException: Cannot invoke "htsjdk.samtools.SAMReadGroupRecord.getReadGroupId()" because the return value of "htsjdk.samtools.SAMRecord.getReadGroup()" is null
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:558)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:270)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)