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Question: Error: failed to load resource reason: invalid class GRanges object: seqnames(x) contains missing values for newer GRCh38 annotations
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gravatar for marcel.schilling
5 weeks ago by
marcel.schilling10 wrote:
library(AnnotationHub)


Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval,
    evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

 

ah <- AnnotationHub()

updating metadata: retrieving 1 resource
|=============================================================================================================| 100%

snapshotDate(): 2017-04-25

 

gr <- query(ah, "GRanges")

 

grch38 <- subset(gr, genome == "GRCh38")

 

grch38

AnnotationHub with 37 records
# snapshotDate(): 2017-04-25
# $dataprovider: Ensembl, Gencode
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded,
#   preparerclass, tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH28606"]]'

            title
  AH28606 | Homo_sapiens.GRCh38.78.gtf
  AH28674 | Homo_sapiens.GRCh38.76.gtf
  AH28743 | Homo_sapiens.GRCh38.79.gtf
  AH28812 | Homo_sapiens.GRCh38.77.gtf
  AH47066 | Homo_sapiens.GRCh38.80.gtf
  ...       ...
  AH53321 | Homo_sapiens.GRCh38.87.gtf
  AH53536 | Homo_sapiens.GRCh38.88.abinitio.gtf
  AH53537 | Homo_sapiens.GRCh38.88.chr.gtf
  AH53538 | Homo_sapiens.GRCh38.88.chr_patch_hapl_scaff.gtf
  AH53539 | Homo_sapiens.GRCh38.88.gtf

 

names(grch38)

 [1] "AH28606" "AH28674" "AH28743" "AH28812" "AH47066" "AH47963" "AH49554" "AH49555" "AH49556" "AH49557" "AH49558"
[12] "AH49559" "AH49560" "AH49561" "AH49562" "AH50308" "AH50377" "AH50841" "AH50842" "AH50843" "AH50844" "AH51011"
[23] "AH51012" "AH51013" "AH51014" "AH51952" "AH51953" "AH51954" "AH51955" "AH53318" "AH53319" "AH53320" "AH53321"
[34] "AH53536" "AH53537" "AH53538" "AH53539"

 

grch38[27:28]

AnnotationHub with 2 records
# snapshotDate(): 2017-04-25
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded,
#   preparerclass, tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH51953"]]'

            title
  AH51953 | Homo_sapiens.GRCh38.86.chr.gtf
  AH51954 | Homo_sapiens.GRCh38.86.chr_patch_hapl_scaff.gtf

 

ens86 <- grch38[["AH51953"]]

Importing File into R ..
require(“rtracklayer”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/58691’
retrieving 1 resource   |=============================================================================================================| 100%

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

using guess work to populate seqinfo
Warning message:
Failed to parse headers:
220-220- Welcome to the Ensembl anonymous FTP site
220-220- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
220-220-
220-220-   Users of the material provided here in advance of submission to
220-220-   public databases should read the Data Release Policy
220-220-   and Guidelines and Conditions on use of Data in the respective data
220-220-   directory.
220-220-
220-220-   Please report any unusual problems you may have with this server
220-220-   via e-mail to webmaster@ensembl.org
220-220-
220-220-   All connections and transfers are logged
220-220-
220-220 (ensembl ftp server)
220
331 Please specify the password.
230 Login successful.
257 "/"
250 Directory successfully changed.
250 Directory successfully changed.
250 Directory successfully changed.
250 Directory successfully changed.
213 20160913145847
229 Entering Extended Passive Mode (|||31017|)
200 Switching to Binary mode.
213 45751175
150 Opening BINARY mode data connection for Homo_sapiens.GRCh3 [... truncated]

 

ens86_chr_patch_hapl_scaff <- grch38[["AH51954"]]

Importing File into R ..
downloading from ‘https://annotationhub.bioconductor.org/fetch/58692’
retrieving 1 resource
|=============================================================================================================| 100%

Error: failed to load resource
  name: AH51954
  title: Homo_sapiens.GRCh38.86.chr_patch_hapl_scaff.gtf
  reason: invalid class “GRanges” object: 'seqnames(x)' contains missing values
In addition: Warning message:
Failed to parse headers:
213 20160913150653
229 Entering Extended Passive Mode (|||39568|)
213 49520204
150 Opening BINARY mode data connection for Homo_sapiens.GRCh38.86.chr_patch_hapl_scaff.gtf.gz (49520204 bytes).
226 Transfer complete.

 

sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 BSgenome_1.44.2
 [3] Biostrings_2.44.2                      XVector_0.16.0
 [5] rtracklayer_1.36.6                     GenomicRanges_1.28.6
 [7] GenomeInfoDb_1.12.3                    IRanges_2.10.5
 [9] S4Vectors_0.14.7                       AnnotationHub_2.8.2
[11] BiocGenerics_0.22.1                    nvimcom_0.9-36
[13] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13                  BiocInstaller_1.26.1          compiler_3.4.2
 [4] bitops_1.0-6                  tools_3.4.2                   zlibbioc_1.22.0
 [7] digest_0.6.12                 bit_1.1-12                    lattice_0.20-35
[10] RSQLite_2.0                   memoise_1.1.0                 tibble_1.3.4
[13] pkgconfig_2.0.1               rlang_0.1.2                   Matrix_1.2-11
[16] DelayedArray_0.2.7            shiny_1.0.5                   DBI_0.7
[19] curl_3.0                      yaml_2.1.14                   GenomeInfoDbData_0.99.0
[22] httr_1.3.1                    grid_3.4.2                    bit64_0.9-7
[25] Biobase_2.36.2                R6_2.2.2                      AnnotationDbi_1.38.2
[28] BiocParallel_1.10.1           XML_3.98-1.9                  blob_1.1.0
[31] matrixStats_0.52.2            GenomicAlignments_1.12.2      Rsamtools_1.28.0
[34] htmltools_0.3.6               SummarizedExperiment_1.6.5    mime_0.5
[37] interactiveDisplayBase_1.14.0 xtable_1.8-2                  httpuv_1.3.5
[40] RCurl_1.95-4.8

 

 

 

 
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by marcel.schilling10
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