I have 6 samples, 3 sets of 2 replicates. Not sure why the error is coming up. Something that seems off is that it says 'computing metrics for 10 samples when I only have 6.

chipObj <- ChIPQC(samples, annotation="hg38")

The error is below.

Checking chromosomes:
[1] "1"
Compiling annotation...
Computing metrics for 10 samples...
list
Bam file has 195 contigs
Error in sampleQC(bamFile = reads, bedFile = peaks, GeneAnnotation = annotation,  : 
  Contigs of interest are not all in Bam file!!
In addition: Warning message:
In if (is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

Let me know if you need any other tests/outputs to help solve this!

Thanks!