sequenza.results() error: Error in seq.default(from = CNt.min/CNn, to = CNt.max/CNn, by = 1/CNn) : 'to' must be a finite number

Question

[Matt]

I'm using sequenza to estimate the cellularity and ploidy of a tumor sample. when I use the *.bam which results from mapping with bwa as the input file, everything is fine. However, if I use the bam file after gatk MarkDuplicates as input file, the sequenza.results() step will raise the error. Has anyone encountered this situation?