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