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I also had this problem. For context, my mcools are generated via hic2mcool from .hic files. hic2mcool has problems converting the latest .hic file format version to .mcool. The bug I know about is that chromosome names get varied numbers of 'chr' prefixes at various resolutions (i.e. 'chrchrchr1', '1', etc.). Perhaps there are also other bugs resulting in this issue?
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