I've been having some difficulty debugging this particular error. When running cn.mops on some soybean data, I get the following error message: res <- exomecn.mops(bamSegmentRanges[1:800,]) Normalizing... Starting local modeling, please be patient... Reference sequence: Gm18 Reference sequence: Gm20 Starting segmentation algorithm... Using "fastseg" for segmentation. Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 6: negative widths are not allowed I have checked the obvious, that is, that width(temp) is strictly positive, and I've even managed to narrow the offending section (or at least one of the offending sections) down to this region: > bamSegmentRanges[795:800,] GRanges with 6 ranges and 6 metadata columns: seqnames ranges strand | Adams Amsoy Harosoy Ogden Tokyo York <rle> <iranges> <rle> | <integer> <integer> <integer> <integer> <integer> <integer> [1] Gm18 [4213632, 4216118] + | 746 349 1602 396 422 511 [2] Gm20 [4213809, 4221748] + | 229 78 670 163 186 215 [3] Gm18 [4218455, 4221721] + | 6 0 20 22 2 14 [4] Gm18 [4222355, 4224539] + | 0 0 131 101 179 152 [5] Gm18 [4231910, 4235860] - | 18 2 25 61 29 41 [6] Gm18 [4239285, 4241479] - | 88 63 253 126 202 192 --- seqlengths: Gm01 Gm02 Gm03 Gm04 ... scaffold_950 scaffold_96 scaffold_973 scaffold_985 NA NA NA NA ... NA NA NA NA that is, when I run res <- exomecn.mops(bamSegmentRanges[1:795,]) the program exits successfully. Here are the results of traceback(): 6: .Call(.NAME, ..., PACKAGE = PACKAGE) 5: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") 4: solveUserSEW0(start = start, end = end, width = width) 3: IRanges(start(inputChr)[segDfChr$start], end(inputChr)[segDfChr$end]) 2: cn.mops(input = input, I = I, classes = classes, priorImpact = priorImpact, cyc = cyc, parallel = parallel, normType = normType, normQu = normQu, norm = norm, lowerThreshold = lowerThreshold, upperThreshold = upperThreshold, minWidth = minWidth, segAlgorithm = segAlgorithm, minReadCount = minReadCount, returnPosterior = returnPosterior, ...) 1: exomecn.mops(temp) and my sessionInfo() is R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] snow_0.3-12 cn.mops_1.6.6 GenomicRanges_1.12.5 IRanges_1.18.3 Biobase_2.20.1 [6] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] Biostrings_2.28.0 bitops_1.0-6 graph_1.38.3 Rgraphviz_2.4.1 Rsamtools_1.12.4 stats4_3.0.2 [7] tools_3.0.2 zlibbioc_1.6.0 Due to the fact that I have no idea what is actually causing the error, I'm having trouble coming up with a reproducible example. Thanks for your help! Susan VanderPlas Iowa State University