Why DepthOfCoverage did not give coverage summary for all my intervals?

Hi,

I am calculating the coverage at intervals listed in my input file by using -L option. I have 89 intervals but only get the coverage for 75 intervals. Why am I missing the rest? The options I used are:
--omitLocusTable --omitPerSampleStats --countType COUNT_FRAGMENTS -ct 30

Thank you

Answers

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