I tried to run ONCOCNV.sh (most recent version) on a set of 9 normal sample alignments to generate a baseline to call CNVs on a set of 8 tumor samples. I used an appropriate tab-delimited BED file (chr, start, end, amplicon ID, 0, and gene name), BAM alignments, and an Ensembl reference genome. All tool requirements were satisfied. However, I was getting the following error with processSamples.R:
running processSamples.R Package 'mclust' version 5.4.5 Type 'citation("mclust")' for citing this R package in publications. PSCBS v0.65.0 successfully loaded. See ?PSCBS for help. Attaching package: ‘PSCBS’ The following objects are masked from ‘package:base’: append, load R.cache v0.13.0 (2018-01-03) successfully loaded. See ?R.cache for help. Loading required package: lattice Loading required package: grid Loading required package: parallel Error in mvnX(data = data, prior = prior) : NA/NaN/Inf in foreign function call (arg 1) Calls: predictClust ... eval -> eval -> mclustBIC -> mvn -> eval -> eval -> mvnX In addition: Warning messages: 1: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != : longer object length is not a multiple of shorter object length 2: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != : longer object length is not a multiple of shorter object length 3: In chrom != "chrM" & chrom != "chrX" & chrom != "chrY" & chrom != : longer object length is not a multiple of shorter object length 4: In rnorm(length(autoInd), 0, sdError[autoInd]) : NAs produced Execution halted
I want to mention that the Control.stats.Processed.txt file from processControls.R contained some fields with missing values (NA) for mean and IC1-3. Replacing those values with arbitrary numbers did not seem to help. Any clues as to what could be causing this error would be much appreciated.