Question

IRanges error loading rsem data into ballgown

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jchenpku • 0

@jchenpku-12342

Last seen 7.6 years ago

I was trying to load rsem output into ballgown but encounter the following error:

Any idea what's wrong? Thanks.

> bg = ballgownrsem(dir="RSEM_Ballgown", samples=phenoData$Sample_Name, gtf,
+                   bamout = "none", meas='all',pData = phenoData)
Sun Feb 12 15:44:50 2017
Sun Feb 12 15:44:51 2017: reading annotation
Sun Feb 12 15:50:06 2017: handling exons
Sun Feb 12 15:50:17 2017: handling introns
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 6: negative widths are not allowed
> traceback()
7: .Call(.NAME, ..., PACKAGE = PACKAGE)
6: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
5: solveUserSEW0(start = start, end = end, width = width)
4: IRanges(start = end(unltrans)[notLast] + 1, end = start(unltrans)[which(notLast) +
       1] - 1)
3: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges,
       strand = strand, mcols = mcols, seqlengths = seqlengths,
       seqinfo = seqinfo)
2: GRanges(seqnames = seqnames(unltrans)[notLast], ranges = IRanges(start = end(unltrans)[notLast] +
       1, end = start(unltrans)[which(notLast) + 1] - 1), strand = strand(unltrans)[notLast])
1: ballgownrsem(dir = "RSEM_Ballgown", samples = phenoData$Sample_Name,
       gtf, bamout = "none", meas = "all", pData = phenoData)

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] IRanges_2.8.1 S4Vectors_0.12.1 BiocGenerics_0.20.0 devtools_1.12.0 dplyr_0.5.0
[6] genefilter_1.56.0 RSkittleBrewer_1.1 ballgown_2.6.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.9                RColorBrewer_1.1-2         GenomeInfoDb_1.10.3        XVector_0.14.0
[5] bitops_1.0-6               tools_3.3.1                zlibbioc_1.20.0            digest_0.6.12
[9] tibble_1.2                 annotate_1.52.1            RSQLite_1.1-2              memoise_1.0.0
[13] nlme_3.1-131               lattice_0.20-34            mgcv_1.8-17                Matrix_1.2-8
[17] DBI_0.5-1                  withr_1.0.2                rtracklayer_1.34.1         Biostrings_2.42.1
[21] grid_3.3.1                 Biobase_2.34.0             R6_2.2.0                   AnnotationDbi_1.36.2
[25] XML_3.98-1.5               survival_2.40-1            BiocParallel_1.8.1         limma_3.30.11
[29] sva_3.22.0                 magrittr_1.5               Rsamtools_1.26.1           GenomicAlignments_1.10.0
[33] splines_3.3.1              GenomicRanges_1.26.2       assertthat_0.1             SummarizedExperiment_1.4.0
[37] xtable_1.8-2               RCurl_1.95-4.8

ballgown • 1.5k views

ADD COMMENT • link updated 7.6 years ago by Jeff Leek ▴ 650 • written 7.6 years ago by jchenpku • 0

score 0 · Answer 1 · 2017-02-13

Hello Can you let me know what gtf file you are using? It seems like there is some problem reading the gtf file which is why you are getting issues with the GRanges. Can you import the genes data with tximport? https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html Best Jeff On Sun, Feb 12, 2017 at 3:10 AM jchenpku [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User jchenpku <https: support.bioconductor.org="" u="" 12342=""/> wrote Question: > IRanges error loading rsem data into ballgown > <https: support.bioconductor.org="" p="" 92389=""/>: > > I was trying to load rsem output into ballgown but encounter the following > error: > > Any idea what's wrong? Thanks. > > > bg = ballgownrsem(dir="RSEM_Ballgown", samples=phenoData$Sample_Name, > gtf, > + bamout = "none", meas='all',pData = phenoData) > Sun Feb 12 15:44:50 2017 > Sun Feb 12 15:44:51 2017: reading annotation > Sun Feb 12 15:50:06 2017: handling exons > Sun Feb 12 15:50:17 2017: handling introns > Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") > : > solving row 6: negative widths are not allowed > > traceback() > 7: .Call(.NAME, ..., PACKAGE = PACKAGE) > 6: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") > 5: solveUserSEW0(start = start, end = end, width = width) > 4: IRanges(start = end(unltrans)[notLast] + 1, end = > start(unltrans)[which(notLast) + > 1] - 1) > 3: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, > strand = strand, mcols = mcols, seqlengths = seqlengths, > seqinfo = seqinfo) > 2: GRanges(seqnames = seqnames(unltrans)[notLast], ranges = IRanges(start > = end(unltrans)[notLast] + > 1, end = start(unltrans)[which(notLast) + 1] - 1), strand = > strand(unltrans)[notLast]) > 1: ballgownrsem(dir = "RSEM_Ballgown", samples = phenoData$Sample_Name, > gtf, bamout = "none", meas = "all", pData = phenoData) > > > sessionInfo() > R version 3.3.1 (2016-06-21) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] IRanges_2.8.1 S4Vectors_0.12.1 BiocGenerics_0.20.0 > devtools_1.12.0 dplyr_0.5.0 > [6] genefilter_1.56.0 RSkittleBrewer_1.1 ballgown_2.6.0 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.9 RColorBrewer_1.1-2 > GenomeInfoDb_1.10.3 XVector_0.14.0 > [5] bitops_1.0-6 tools_3.3.1 > zlibbioc_1.20.0 digest_0.6.12 > [9] tibble_1.2 annotate_1.52.1 > RSQLite_1.1-2 memoise_1.0.0 > [13] nlme_3.1-131 lattice_0.20-34 > mgcv_1.8-17 Matrix_1.2-8 > [17] DBI_0.5-1 withr_1.0.2 > rtracklayer_1.34.1 Biostrings_2.42.1 > [21] grid_3.3.1 Biobase_2.34.0 > R6_2.2.0 AnnotationDbi_1.36.2 > [25] XML_3.98-1.5 survival_2.40-1 > BiocParallel_1.8.1 limma_3.30.11 > [29] sva_3.22.0 magrittr_1.5 > Rsamtools_1.26.1 GenomicAlignments_1.10.0 > [33] splines_3.3.1 GenomicRanges_1.26.2 > assertthat_0.1 SummarizedExperiment_1.4.0 > [37] xtable_1.8-2 RCurl_1.95-4.8 > ------------------------------ > > Post tags: ballgown > > You may reply via email or visit IRanges error loading rsem data into ballgown >