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I am trying to get the ipdRatio and modified bases information from a PacBio bam file which is sorted and indexed. The command I'm running is:

ipdSummary sorted_chr21_0_100000.bam --reference $REF_path/$REF_FILE_NAME.fasta --referenceWindow 20:0-100000 --identify m6A,m4C,m5C_TET --methylFraction --outfile sorted_chr21_0_100000;

I get the following warning message:

RuntimeWarning: Non-unique read group integer IDs found - some features may be restricted warnings.warn("Non-unique read group integer IDs found - some features may be restricted", RuntimeWarning)

My question is which types of features might be restricted if my read groups are not unique?

I am not sure how critical it could be.

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