Hi,

I'm trying to perform a CNV analysis on 12 BAM files from WES data using cn.mops package. BAM files were aligned to GChr38, markduplicated and recalibrated following the GATK best practices.

BAMFiles <- grep('84|93|117|134|350|454', list.files(path = 'results/Preprocessing/', pattern = '*.recal.bam$', recursive = T, full.names = T), value = T)
segments <- read.table("data/exons_plus50.bed",sep="\t",as.is=TRUE)
gr <- GRanges(segments[,1],IRanges(segments[,2],segments[,3]))
gr2 <- tidyChromosomes(
    gr,
    keep.X = T,
    keep.Y = T,
    keep.M = FALSE,
    keep.nonstandard = F,
    genome = NULL
)
X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr2, parallel = 16)

The targets bed file (data/exons_plus50.bed) contains all the exons plus their flanking 50 bp for the corresponding human genome version. I had to exclude the M and the non-standard (haplotypes) chromosomes because the getSegmentReadCountsFromBAM function raises an error otherwise.

So far it ran as expected, without errors.

However, when running exomecn.mops function, it prompts the following:

resCNMOPS <- exomecn.mops(X, parallel = 16)
Normalizing...
Starting local modeling, please be patient...  
Reference sequence:  chr1
Reference sequence:  chr2
Reference sequence:  chr3
Reference sequence:  chr4
Reference sequence:  chr5
Reference sequence:  chr6
Reference sequence:  chr7
Reference sequence:  chr8
Reference sequence:  chr9
Reference sequence:  chrX
Reference sequence:  chrY
Reference sequence:  chr10
Reference sequence:  chr11
Reference sequence:  chr12
Reference sequence:  chr13
Reference sequence:  chr14
Reference sequence:  chr15
Reference sequence:  chr16
Reference sequence:  chr17
Reference sequence:  chr18
Reference sequence:  chr19
Reference sequence:  chr20
Reference sequence:  chr21
Reference sequence:  chr22
Starting segmentation algorithm...
Using "fastseg" for segmentation.
Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") : 
  each range must have an end that is greater or equal to its start minus one

Setting the algorithm to DNACopy gives the same error.

I've tried with the lifted over (GRCh37 -> GRCh38) version of the baits BED file provided by the vendor (the original one has the hg19 version) for the corresponding kit (here) instead of the targets file (containing all exons), but the error persists.

I appreciate any clue about this issue.

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BRGenomics_1.6.0     rtracklayer_1.54.0   cn.mops_1.40.0       GenomicRanges_1.46.1
[5] GenomeInfoDb_1.30.1  IRanges_2.28.0       S4Vectors_0.32.4     BiocGenerics_0.40.0