Question

error in exomeCopy - IRanges?

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Lescai, Francesco ▴ 380

@lescai-francesco-5078

Last seen 7.1 years ago

Denmark

Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Calls: compileCopyCountSegments ... RangedData -> is -> IRanges -> solveUserSEW0 -> .Call2 -> .Call Execution halted any idea is much appreciated. thanks, Francesco > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] exomeCopy_1.2.0 Rsamtools_1.8.5 Biostrings_2.24.1 [4] GenomicRanges_1.8.7 IRanges_1.14.4 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0

IRanges exomeCopy IRanges exomeCopy • 3.1k views

ADD COMMENT • link updated 13.2 years ago by love ▴ 150 • written 13.2 years ago by Lescai, Francesco ▴ 380

score 0 · Answer 1 · 2012-08-06

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love ▴ 150

@love-5173

Last seen 11.2 years ago

On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco<f.lescai@ucl.ac.uk <mailto:f.lescai@ucl.ac.uk="">>wrote: Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Hi Francesco, I have seen this error before when the target GRanges has duplicate or unsorted regions, and fixed this in the devel branch. You could try to reduce the target GRanges first, before counting sample read counts. Could you try: all.equal(target, reduce(target)) If these are in fact equal, you can send me the fit.list object and I can try to debug. best, Mike [[alternative HTML version deleted]]

ADD COMMENT • link 13.2 years ago love ▴ 150

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Thanks Mike, that seems exactly the case. Does it mean I have to re-run both the reads counting and computation? or can I fix it somehow? thanks, Francesco On 6 Aug 2012, at 23:46, Mike Love <love@molgen.mpg.de<mailto:love@molgen.mpg.de>> wrote: On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco <f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>> wrote: Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Hi Francesco, I have seen this error before when the target GRanges has duplicate or unsorted regions, and fixed this in the devel branch. You could try to reduce the target GRanges first, before counting sample read counts. Could you try: all.equal(target, reduce(target)) If these are in fact equal, you can send me the fit.list object and I can try to debug. best, Mike ---------------------------------------------------------------------- ----------- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development & Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk> phone: +44.(0)207.905.2274 [ext: 2274] ---------------------------------------------------------------------- ---------- [[alternative HTML version deleted]]

ADD REPLY • link 13.2 years ago Lescai, Francesco ▴ 380

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On 08/07/12 15:41, Lescai, Francesco wrote: Thanks Mike, that seems exactly the case. Does it mean I have to re-run both the reads counting and computation? or can I fix it somehow? thanks, Francesco On 6 Aug 2012, at 23:46, Mike Love <[1]love at molgen.mpg.de> wrote: On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco <[2]f.lescai at ucl.ac.uk> wrote: Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Hi Francesco, I have seen this error before when the target GRanges has duplicate or unsorted regions, and fixed this in the devel branch. You could try to reduce the target GRanges first, before counting sample read counts. Could you try: all.equal(target, reduce(target)) If these are in fact equal, you can send me the fit.list object and I can try to debug. best, Mike Hi Francesco, Sorry I should have written: all.equal(target, reduce(target, min.gapwidth=0)) ...as adjacent ranges are fine. It is probably easier to re-run counting after reducing the target with min.gapwidth=0. There could be complicated overlapping ranges generated if you have overlapping but not identical regions in the original target file. Mike References 1. mailto:love at molgen.mpg.de 2. mailto:f.lescai at ucl.ac.uk

ADD REPLY • link 13.2 years ago love ▴ 150

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I can confirm reducing the target removes that error. I simply added in my script target <- reduce(target) target.sub <- subdivideGRanges(target) thanks very much for your help, Francesco On 7 Aug 2012, at 15:51, Michael Love <love@molgen.mpg.de<mailto:love@molgen.mpg.de>> wrote: On 08/07/12 15:41, Lescai, Francesco wrote: Thanks Mike, that seems exactly the case. Does it mean I have to re-run both the reads counting and computation? or can I fix it somehow? thanks, Francesco On 6 Aug 2012, at 23:46, Mike Love <love@molgen.mpg.de<mailto:love@molgen.mpg.de>> wrote: On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco <f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>> wrote: Hi there, I'm having an error in exomeCopy when I count the CNVs. No previous error in any of the other steps illustrated in the vignette the computation of the fit list didn't give any warning and it seems to be formatted correctly > fit.list[[1]][1] $`1` ExomeCopy object sample name: UCLG_502_ATCACG_L003 percent normal state: 79.87% > summary(fit.list$UCLG_502_ATCACG_L003$`1`) Length Class Mode 1 ExomeCopy S4 but then I get > compiled.segments <- compileCopyCountSegments(fit.list) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 1: negative widths are not allowed Hi Francesco, I have seen this error before when the target GRanges has duplicate or unsorted regions, and fixed this in the devel branch. You could try to reduce the target GRanges first, before counting sample read counts. Could you try: all.equal(target, reduce(target)) If these are in fact equal, you can send me the fit.list object and I can try to debug. best, Mike Hi Francesco, Sorry I should have written: all.equal(target, reduce(target, min.gapwidth=0)) ...as adjacent ranges are fine. It is probably easier to re-run counting after reducing the target with min.gapwidth=0. There could be complicated overlapping ranges generated if you have overlapping but not identical regions in the original target file. Mike ---------------------------------------------------------------------- ----------- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development & Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk> phone: +44.(0)207.905.2274 [ext: 2274] ---------------------------------------------------------------------- ---------- [[alternative HTML version deleted]]

ADD REPLY • link 13.2 years ago Lescai, Francesco ▴ 380