Error while using a BED file

[mokhouja]

Hi,

I am a complete newbie in data science and R but I have been trying to use the script to analyze CNA for a targeted capture sequencing in cfDNA as following:

/scratch/scripts/runIchorCNA.R --id tumor_sample   --WIG test.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5   
--gcWig /scratch/inst/extdata/gc_hg38_1000kb.wig   --mapWig /scratch/inst/extdata/map_hg38_1000kb.wig   
--centromere /scratch/inst/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt   
--includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)"   --estimateNormal True --estimatePloidy True 
--es[AtimateScPrevalence True   --scStates "c(1,3)" --txnE 0.9999 --txnStrength 10000 --outDir ./ 
--exons.bed  CNV.target.bed --genomeBuild hg38

and I am keep getting the following error:

Correcting Tumour
Removed 121 bins near centromeres.
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Filtering low uniqueness regions with mappability score < 0.9
Removed 1 bins near centromeres.
Determining gender...Gender female
Outputting to: .//tumor_sample.correctedDepth.txt
Warning messages:
1: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  span too small.   fewer data values than degrees of freedom.
2: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  pseudoinverse used at 0.36574
3: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  neighborhood radius 0.0032647
4: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  reciprocal condition number  0
5: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  There are other near singularities as well. 0.0033244
6: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
runEM: Initialization
runEM iter1: Expectation
Error in runEM(dataMat, chr, chrInd, param, maxiter, verbose, estimateNormal = estimateNormal,  : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Calls: HMMsegment -> runEM
Execution halted

and when running without using a bed file it works but gives the following warnings:

1: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
2: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
3: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
4: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

my .BED file looks like this

Chr	start	end
1	23558903	23559184
1	23559184	23559465
1	26696365	26696631

I'll appreciate your advice.
Bests,
Mouhamad