Hi,

I have been using cn.mops successfully using the following commands:

bamDataRanges <- getReadCountsFromBAM(BAMFiles, refSeqName=readLines("Chr_list.txt"), WL=1000)

results <- calcIntegerCopyNumbers(cn.mops(bamDataRanges))

segm <- as.data.frame(segmentation(results))
CNVs <- as.data.frame(cnvs(results))
CNVRegions <- as.data.frame(cnvr(results))

However, im now running it on additional bam files and i get the following error:

Error in value[[3L]](cond) : 
  failed to open BamFile: failed to load BAM index
  file: A27.realigned.rmdup.bam
Calls: getReadCountsFromBAM ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  [bam_index_load] fail to load BAM index.
Execution halted

i have checked the header of my bam file and looks fine, would you please help me in trying to fix the error?

Thanks for your time and support,

Laura

I think this is not a problem of cn.mops but of an internally used function (Rsamtools?).

• Could you run "traceback" right after the error occurs and post the result here.
• Please check if for each BAM file, there exists an BAI (index) file. This can be generated using samtools

Regards,
Günter

Thanks for your prompt answer, here is the traceback:

> traceback()
11: stop("failed to open BamFile: ", conditionMessage(err))
10: value[[3L]](cond)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({
       .io_check_exists(path(con))
       index <- sub("\\.bai$", "", index(con, asNA = FALSE))
       con$.extptr <- .Call(.bamfile_open, path(con), index, "rb")
   }, error = function(err) {
       stop("failed to open BamFile: ", conditionMessage(err))
   })
6: open.BamFile(BamFile(file, index), "rb")
5: open(BamFile(file, index), "rb")
4: scanBam(bam.file, param = ScanBamParam(what = scan.what, which = range(granges.subset)))
3: scanBam(bam.file, param = ScanBamParam(what = scan.what, which = range(granges.subset)))
2: exomeCopy::countBamInGRanges(bam.file = BAMFiles[i], granges = GR,
       ...)
1: getReadCountsFromBAM(BAMFiles, refSeqName = readLines("/users/lbuggiotti/WGresRussia/cn.MOPS/Chr_list.txt"),
       WL = 1000)

Moreover i have BAI file for each bam created by using samtools.

Thanks again,

Laura

Ok, this is a problem either with your BAM files or with Rsamtools with the function "scanBam". Please contact the maintainers of Rsamtools.