Error Running Bmr Calc-Covg

Question

[lili]

Hello,

I'm trying to run bmr calc-covg and got an warning message:

[fai_fetch] Warning - Reference 1 not found in FASTA file, returning empty sequence Failed to execute: calcRoiCovg ..,

I checked my ROI file to make sure the format is fine. The chr name only has numbers I also changed the fasta file so that the sequence header match the chr name in ROI

What could caused the error?

Thanks!

Answer 1

[Chris Miller]

Do all of your chromosome names match between the roi file, fasta, and bam? This includes MT/M and the short alternate haplotypes with names like chr6_cox or GL.1234