Dear Silvia, Could you please send me the test data and code that resulted in this error message? Please also send me your session information as well. Thanks! Best regards, Julie On 1/14/13 6:33 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> wrote: Hello! I have a problem with the function mentioned above (should be solve_user_SEW invoked by getAllPeakSequence) and I hope you can help me. I get an error: "in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (130043477) is > refwidth + 1" I've already read in some mailing lists that this is known but I did not find any solution for that. Many thanks in advance, Silvia [[alternative HTML version deleted]]

Silvia, I understand that you cannot send the whole dataset. Could you please just send me the chromosome,strand, start and end information for the row that caused the problem so that I can try to reproduce the error? Also, could you please update ChIPpeakAnno to 2.6 and see if that resolves the problem http://www.bioconductor.org/packages/2.11/bioc/html/ChIPpeakAnno.html? Thanks! Best regards, Julie On 1/14/13 11:23 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> wrote: Hello, thanks for the quick response. Unfortunately I cannot supply the data, but the session info is the following: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] coda_0.15-2 rGADEM_2.4.0 [3] seqLogo_1.22.0 cureos_0.3 [5] multicore_0.1-7 BayesPeak_1.8.0 [7] org.Mm.eg.db_2.7.1 rtracklayer_1.16.3 [9] ShortRead_1.14.4 latticeExtra_0.6-24 [11] RColorBrewer_1.0-5 Rsamtools_1.8.6 [13] lattice_0.20-10 BSgenome.Mmusculus.UCSC.mm9_1.3.17 [15] BiocInstaller_1.4.9 ChIPpeakAnno_2.4.0 [17] limma_3.12.3 org.Hs.eg.db_2.7.1 [19] GO.db_2.7.1 RSQLite_0.11.2 [21] DBI_0.2-5 AnnotationDbi_1.18.4 [23] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0 [25] GenomicRanges_1.8.13 Biostrings_2.24.1 [27] IRanges_1.14.4 multtest_2.12.0 [29] Biobase_2.16.0 biomaRt_2.12.0 [31] BiocGenerics_0.2.0 gplots_2.11.0 [33] MASS_7.3-22 KernSmooth_2.23-8 [35] caTools_1.13 bitops_1.0-4.1 [37] gdata_2.12.0 gtools_2.7.0 loaded via a namespace (and not attached): [1] hwriter_1.3 RCurl_1.95-1.1 splines_2.15.0 stats4_2.15.0 [5] survival_2.36-14 tools_2.15.0 XML_3.95-0.1 zlibbioc_1.2.0 I ithink it should be related to IRanges package... My output.1 data object (used as input when the problem occurs) has the following start ranges and width range(output.1$ranges@start) [1] 2999950 194976340 range(output.1$ranges@width) [1] 101 3551 Many thanks! 2013/1/14 Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> Dear Silvia, Could you please send me the test data and code that resulted in this error message? Please also send me your session information as well. Thanks! Best regards, Julie On 1/14/13 6:33 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com <http:="" silvia.heyde@gmail.com=""> > wrote: Hello! I have a problem with the function mentioned above (should be solve_user_SEW invoked by getAllPeakSequence) and I hope you can help me. I get an error: "in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (130043477) is > refwidth + 1" I've already read in some mailing lists that this is known but I did not find any solution for that. Many thanks in advance, Silvia [[alternative HTML version deleted]]

Silvia, That is great! Thanks for sharing the information! Just to remind you that the genome version you used for getting the coordinates need to match the genome version for getting the sequence from these coordinates. If you have used mm10 for mapping, then mm10 is the right one for retrieving sequence. However, if you have used mm9 for mapping, then mm9 would be the genome version fro retrieving sequence. Best regards, Julie On 1/15/13 7:58 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> wrote: Obviously the old mm-version was the problem, as now (2.6.0 + mm10) I just get 2 warnings but no errors: Warning messages: 1: In remove(list = objname, envir = cache) : object 'chr10' not found 2: In remove(list = objname, envir = cache) : object 'chr9' not found 2013/1/15 Silvia von der Heyde <silvia.heyde@gmail.com> I've just recognized that there is already reference genome "mm10". So maybe the error disappears. I am just running my whole script again. I will inform you in case of persisting error! Many thanks so far! 2013/1/15 Silvia von der Heyde <silvia.heyde@gmail.com> Hi, here is the error I get when applying it on 2.6.0: > library(BSgenome.Mmusculus.UCSC.mm9) > seqShort.1<-getAllPeakSequence(output.1, upstream = 25, downstream = 25, genome=Mmusculus) Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (130043452) is > refwidth + 1 > output.1[1,] RangedData with 1 row and 1 value column across 21 spaces space ranges | PP <factor> <iranges> | <numeric> 1 chr1 [3001340, 3001590] | 0.8543214 2013/1/14 Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> Silvia, I reproduced the same error by trying to fetch a sequence from coordinates that are greater than the reference chromosome length. So I suspect that your dataset contains coordinates beyond the ranges of the reference chromosome. Please let me know whether this is the culprit. Thanks! Best regards, Julie On 1/14/13 11:56 AM, "Lihua Julie Zhu" <julie.zhu@umassmed.edu> wrote: > Silvia, > > I understand that you cannot send the whole dataset. Could you please just > send me the chromosome,strand, start and end information for the row that > caused the problem so that I can try to reproduce the error? Also, could you > please update ChIPpeakAnno to 2.6 and see if that resolves the problem > http://www.bioconductor.org/packages/2.11/bioc/html/ChIPpeakAnno.html? Thanks! > > Best regards, > > Julie > > > On 1/14/13 11:23 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> wrote: > > Hello, > > thanks for the quick response. Unfortunately I cannot supply the data, but the > session info is the following: > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] coda_0.15-2 rGADEM_2.4.0 > [3] seqLogo_1.22.0 cureos_0.3 > [5] multicore_0.1-7 BayesPeak_1.8.0 > [7] org.Mm.eg.db_2.7.1 rtracklayer_1.16.3 > [9] ShortRead_1.14.4 latticeExtra_0.6-24 > [11] RColorBrewer_1.0-5 Rsamtools_1.8.6 > [13] lattice_0.20-10 BSgenome.Mmusculus.UCSC.mm9_1.3.17 > [15] BiocInstaller_1.4.9 ChIPpeakAnno_2.4.0 > [17] limma_3.12.3 org.Hs.eg.db_2.7.1 > [19] GO.db_2.7.1 RSQLite_0.11.2 > [21] DBI_0.2-5 AnnotationDbi_1.18.4 > [23] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0 > [25] GenomicRanges_1.8.13 Biostrings_2.24.1 > [27] IRanges_1.14.4 multtest_2.12.0 > [29] Biobase_2.16.0 biomaRt_2.12.0 > [31] BiocGenerics_0.2.0 gplots_2.11.0 > [33] MASS_7.3-22 KernSmooth_2.23-8 > [35] caTools_1.13 bitops_1.0-4.1 > [37] gdata_2.12.0 gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] hwriter_1.3 RCurl_1.95-1.1 splines_2.15.0 stats4_2.15.0 > [5] survival_2.36-14 tools_2.15.0 XML_3.95-0.1 zlibbioc_1.2.0 > > I ithink it should be related to IRanges package... > My output.1 data object (used as input when the problem occurs) has the > following start ranges and width > range(output.1$ranges@start) > [1] 2999950 194976340 > range(output.1$ranges@width) > [1] 101 3551 > > Many thanks! > > 2013/1/14 Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> > Dear Silvia, > > Could you please send me the test data and code that resulted in this error > message? Please also send me your session information as well. Thanks! > > Best regards, > > Julie > > > > On 1/14/13 6:33 AM, "Silvia von der Heyde" <silvia.heyde@gmail.com> <http: silvia.heyde@gmail.com=""> > wrote: > > Hello! > > I have a problem with the function mentioned above (should be solve_user_SEW > invoked by getAllPeakSequence) and I hope you can help me. > I get an error: > "in .Call2("solve_user_SEW", refwidths, start, end, width, > translate.negative.coord, : solving row 1: 'allow.nonnarrowing' is FALSE and > the supplied start (130043477) is > refwidth + 1" > I've already read in some mailing lists that this is known but I did not find > any solution for that. > > Many thanks in advance, > Silvia > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]