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Question: IRanges error loading rsem data into ballgown
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gravatar for jchenpku
17 months ago by
jchenpku0
jchenpku0 wrote:

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          

ADD COMMENTlink modified 17 months ago by Jeff Leek520 • written 17 months ago by jchenpku0
0
gravatar for Jeff Leek
17 months ago by
Jeff Leek520
United States
Jeff Leek520 wrote:
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 >
ADD COMMENTlink written 17 months ago by Jeff Leek520
Another possibility: is this a prokaryotic assembly? (Ballgown doesn't work if there isn't any intronic data present, unfortunately). On Mon, Feb 13, 2017 at 12:59 PM, Jeff Leek [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Jeff Leek <https: support.bioconductor.org="" u="" 5015=""/> wrote Answer: > IRanges error loading rsem data into ballgown > <https: support.bioconductor.org="" p="" 92389="" #92467="">: > > 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 <https: support.bioconductor.org="" p="" 92389=""/> > > > ------------------------------ > > Post tags: ballgown > > You may reply via email or visit https://support.bioconductor. > org/p/92389/#92467 >
ADD REPLYlink written 17 months ago by Alyssa Frazee190
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