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Question: bad restore file magic number with AnnotationHub
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gravatar for jason.serviss
12 months ago by
jason.serviss0 wrote:

I am failing to load ENCODE RNAseq expression data with after downloading via AnnotationHub.

library(AnnotationHub)
ah = AnnotationHub()
dm <- query(ah, c("EncodeDCC", "Homo sapiens"))
dm["AH1376"]

 

AnnotationHub with 1 record

# snapshotDate(): 2016-11-15 
# names(): AH1376
# $dataprovider: EncodeDCC
# $species: Homo sapiens
# $rdataclass: GRanges
# $title: wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV7
# $description: 
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: BED
# $sourceurl: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLo...
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: c("011WC,012WC", "HeLa-S3", "wgEncodeCshlLongRnaSeq", "RnaSeq", "ENCODE Mar 2012 Freeze",
#   "2011-07-13", "2012-04-13", "wgEncodeEH000173", "GSM765402", "Gingeras", "CSHL",
#   "LID16633,LID16634", "iIDR", "cell", "9b6a25c6c8e577edf94e8a28f41f0f3a", "wgEncode", "2x76D",
#   "longPolyA", "Illumina_GA2x", "2e+06", "Nist14", "4583", "gtf", "GeneGencV7") 
# retrieve record with 'object[["AH1376"]]' 

 

out <- dm[["AH1376"]]

require(“GenomicRanges”)

downloading from ‘https://annotationhub.bioconductor.org/fetch/1376’
retrieving 1 resource
  |======================================================================================================| 100%
Error: failed to load resource
  name: AH1376
  title: wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV7
  reason: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘1376’ has magic number 'chr16'
  Use of save versions prior to 2 is deprecated

sessionInfo()

R version 3.3.2 (2016-10-31)

Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] GenomicRanges_1.26.1 GenomeInfoDb_1.10.1  IRanges_2.8.1        S4Vectors_0.12.0     AnnotationHub_2.6.1 
[6] BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   digest_0.6.10                 mime_0.5                     
 [4] R6_2.2.0                      xtable_1.8-2                  DBI_0.5-1                    
 [7] RSQLite_1.0.0                 BiocInstaller_1.24.0          httr_1.2.1                   
[10] zlibbioc_1.20.0               XVector_0.14.0                curl_2.2                     
[13] Biobase_2.34.0                shiny_0.14.2                  httpuv_1.3.3                 
[16] AnnotationDbi_1.36.0          htmltools_0.3.5               interactiveDisplayBase_1.12.0

 

Is there a known problem here or have I missed something essential? Thanks in advance for any help you can offer!

ADD COMMENTlink modified 11 months ago by Valerie Obenchain ♦♦ 6.4k • written 12 months ago by jason.serviss0

Thanks for posting this bug. We are looking into it.

Valerie

ADD REPLYlink written 12 months ago by Valerie Obenchain ♦♦ 6.4k
0
gravatar for Valerie Obenchain
11 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

Hi,

I'm finally back with an answer. A similar question came up which I've responded to here:

A: AnnotationHub: two broad peaks from same url are not the same

The file you had problems with was saved with the wrong file extension (.Rda when it was really a gff). It was one of a group of files with several problems either in how the data were processed or how the metadata were specified. I gave a more complete answer on the other post but the gist is that these resources were too dammaged to fix and have been removed from the hub. Similar resources are available via query().

Thanks for reporting this.

Valerie

ADD COMMENTlink written 11 months ago by Valerie Obenchain ♦♦ 6.4k
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