annotatr GRanges Error
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@cguzmanroma-8981
Last seen 5.9 years ago
United States

Am receiving this error and not sure how to continue. I am trying to annotate my ChIP-seq peaks to various loci and am using the 'annotatr' package.

Workflow:

library(annotatr)

data <- read_regions(con = "TRIM28_MACS2.broadPeak.forR.bed",
                     genome = 'hg38', format = 'bed')

annots <- c("hg38_basicgenes", "hg38_genes_intergenic",
            "hg38_genes_firstexons", "hg38_genes_intronexonboundaries", "hg38_lncrna_gencode")

annotations <- build_annotations(genome = "hg38",
                                 annotations = annots)

At this point I receive the following error:

'select()' returned 1:1 mapping between keys and columns
Building promoters...
Building 1to5kb upstream of TSS...
Building intergenic...
Building 5UTRs...
Building 3UTRs...
Building exons...
Building first exons...
Building introns...
Building intron exon boundaries...
updating metadata: retrieving 1 resource
  |===========================================================================================| 100%
snapshotDate(): 2016-10-11
Building lncRNA transcripts...
require(“rtracklayer”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/56279’
retrieving 1 resource
  |===========================================================================================| 100%
Error in file(file, "rt") : cannot open connection
In addition: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 131 out-of-bound ranges located on sequences chr1_GL383518v1_alt,
  chr2_GL383522v1_alt, chr5_GL339449v2_alt, chr5_KI270795v1_alt, chr5_KI270898v1_alt,
  chr6_KI270797v1_alt, chr6_KI270798v1_alt, chr6_KI270801v1_alt, chr7_GL383534v2_alt,
  chr7_KI270803v1_alt, chr7_KI270806v1_alt, chr7_KI270809v1_alt, chr8_KI270821v1_alt,
  chr9_GL383540v1_alt, chr9_GL383541v1_alt, chr11_KI270902v1_alt, chr12_GL383551v1_alt,
  chr12_GL383553v2_alt, chr12_KI270834v1_alt, chr14_KI270847v1_alt, chr15_KI270850v1_alt,
  chr16_KI270854v1_alt, chr17_JH159146v1_alt, chr17_JH159147v1_alt, chr17_KI270857v1_alt,
  chr17_KI270860v1_alt, chr19_GL383575v2_alt, chr19_KI270866v1_alt, chr19_KI270884v1_alt,
  chr19_KI270885v1_alt, chr19_KI270889v1_alt, chr19_KI270890v1_alt, chr19_KI270891v1_alt,
  chr19_KI270915v1_alt, chr19_KI270916v1_alt, chr19_KI270919v1_alt, chr19_KI270922v1_alt,
  chr19_KI270929v1_alt, chr19_KI270930v1_alt, chr19_KI270931v1_alt, chr19_KI270932v1_alt,
  chr19_KI270933v1_alt,  [... truncated]

Any ideas?

annotatr • 1.2k views
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rcavalca ▴ 140
@rcavalca-7718
Last seen 4.0 years ago
United States
Hello, Thanks for using annotatr. It looks like there is a GRanges warning that some ranges are out of the chromosome bounds. This is normal because some of the annotations extend regions and are then trimmed. The error looks to be related to the lncRNA resource. > Error in file(file, "rt") : cannot open connection This is related to a wider problem in the GenomeInfoDb::Seqinfo() function. Recently NCBI changed their server directory structure, causing this function to fail. I've alerted the bioc-devel mailing list and they are working to fix this. I will update you when it's fixed, and push an update to annotatr requiring the new package version. I hope it's sometime next week because I have some updates to annotatr I wanted to push. For now, to continue using annotatr, you should drop the 'hg38_lncrna_gencode' annotations; my test works without it. I should also warn you that random regions are also out of commission because of this same problem. Sorry for the inconvenience, Raymond
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Entering edit mode
rcavalca ▴ 140
@rcavalca-7718
Last seen 4.0 years ago
United States

Hello,

I wanted to follow up to let you know GenomeInfoDb has been updated to 1.10.3 on the release branch and 1.11.9 on the devel branch. The update fixes the issue causing the error in both. Since they haven't made their way through the Bioconductor build system, I installed the release version with 

devtools::install_github('Bioconductor-mirror/GenomeInfoDb@release-3.4')

and have updated annotatr to require at least this package version. That will make it's way through the Bioconductor build system shortly after GenomeInfoDb.

Let me know if you continue to have issues,

Raymond

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