Unable to produce .cnr files about cnvkit HOT 2 OPEN

Cnvkit performs some internal filtering (based on gc, log2, spread and depth=0) of bins that might skew the CNV calling results. My understanding is that the cnvkit smoothing fails (which takes care of bias corrections) when there are less than 2 bins left after filtering (which occurs separately for target and anti-target bins). Since your problem seems to be with the anti-target bins you could try to disable the usage of anti-target bins. I am not entirely sure, since I don't usually use the batch command, but I think you could disable anti-target bins by using --method amplicon.

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thank you for your input. Should I expect to see the low coverage warning for anti-target analysis as these are the non-targeted regions? Also, it always seems to be that one bin from the anti-target file that causes the error, would it be wise to drop that row from reference.cnn for the analysis to complete?

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