Question

rtracklayer: error in importing bigwig file in r in windows

1

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mzwanelen ▴ 10

@mzwanelen-22944

Last seen 20 months ago

Canada

I cant import bigwig file in r

Code: map_hg18 <- import("wgEncodeCrgMapabilityAlign100mer",format="BigWig")

Error: Error in seqinfo(ranges) : UCSC library operation failed In addition: Warning message: In seqinfo(ranges) : No such file or directory mustOpenFd: Can't open wgEncodeCrgMapabilityAlign100mer to read

Session info:

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C LCTIME=English_United States.1252

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

other attached packages: [1] Rsamtools2.2.3 BSgenome.Hsapiens.UCSC.hg181.3.1000 BSgenome1.54.0
[4] rtracklayer1.46.0 Biostrings2.54.0 XVector0.26.0
[7] HiCDataHumanIMR901.6.0 HiTC1.30.0 GenomicRanges1.38.0
[10] GenomeInfoDb1.22.0 IRanges2.20.2 S4Vectors0.24.3
[13] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] zlibbioc1.32.0 GenomicAlignments1.22.1 BiocParallel1.20.1 lattice0.20-40
[5] tools3.6.2 SummarizedExperiment1.16.1 grid3.6.2 Biobase2.46.0
[9] matrixStats0.55.0 Matrix1.2-18 GenomeInfoDbData1.2.2 BiocManager1.30.10
[13] RColorBrewer1.1-2 bitops1.0-6 RCurl1.98-1.1 DelayedArray0.12.2
[17] compiler3.6.2 XML3.99-0.3

rtracklayer bigwig file • 2.6k views

ADD COMMENT • link updated 3.2 years ago by Leonardo Collado Torres ★ 1.1k • written 4.8 years ago by mzwanelen ▴ 10

1

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As far as I know, rtracklayer::import.bw() does not work on Windows OS.

ADD REPLY • link 4.7 years ago Leonardo Collado Torres ★ 1.1k

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No, it works on Windows:

> z <- import("hg38.phastCons4way.bw", which = GRanges("chr1:1-1e5"))
> z
GRanges object with 17794 ranges and 1 metadata column:
          seqnames    ranges strand |               score
             <Rle> <IRanges>  <Rle> |           <numeric>
      [1]     chr1     18871      * | 0.00800000037997961
      [2]     chr1     18872      * | 0.00400000018998981
      [3]     chr1     36851      * |                   0
      [4]     chr1     40856      * | 0.00100000004749745
      [5]     chr1     40857      * |  0.0020000000949949
      ...      ...       ...    ... .                 ...
  [17790]     chr1     71832      * |  0.0160000007599592
  [17791]     chr1     71833      * |  0.0149999996647239
  [17792]     chr1     71834      * |  0.0120000001043081
  [17793]     chr1     71835      * | 0.00700000021606684
  [17794]     chr1     98378      * |                   0
  -------
  seqinfo: 244 sequences from an unspecified genome
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] rtracklayer_1.46.0   GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 
[4] IRanges_2.20.2       S4Vectors_0.24.3     BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] matrixStats_0.55.0          lattice_0.20-38            
 [3] XML_3.99-0.3                Rsamtools_2.2.1            
 [5] Biostrings_2.54.0           GenomicAlignments_1.22.1   
 [7] bitops_1.0-6                grid_3.6.1                 
 [9] zlibbioc_1.32.0             XVector_0.26.0             
[11] Matrix_1.2-17               BiocParallel_1.20.1        
[13] tools_3.6.1                 Biobase_2.46.0             
[15] RCurl_1.98-1.1              DelayedArray_0.12.2        
[17] compiler_3.6.1              SummarizedExperiment_1.16.1
[19] GenomeInfoDbData_1.2.2     
>

ADD REPLY • link 4.7 years ago James W. MacDonald 67k

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Awesome, thanks James! This didn't use to be the case, but I'm happy to hear that it works now. Looks like I need to remove warnings such as https://github.com/lcolladotor/derfinder/blob/master/R/loadCoverage.R#L222-L224 from my code.

ADD REPLY • link 4.7 years ago Leonardo Collado Torres ★ 1.1k

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I'm currently experiencing the same. I'm on rtracklayer version 1.53.1.

On ubuntu:

> import("https://rlbase-data.s3.amazonaws.com/coverage/SRX7671349_hg38.bw", which = GRanges("chr1:1e6-1.5e6"))
GRanges object with 11 ranges and 1 metadata column:
       seqnames          ranges strand |     score
          <Rle>       <IRanges>  <Rle> | <numeric>
   [1]     chr1 1000000-1014050      * |         0
   [2]     chr1 1014051-1014250      * |         1
   [3]     chr1 1014251-1110000      * |         0
   [4]     chr1 1110001-1110050      * |         1
   [5]     chr1 1110051-1110100      * |         0
   [6]     chr1 1110101-1110150      * |         1
   [7]     chr1 1110151-1472500      * |         0
   [8]     chr1 1472501-1472600      * |         1
   [9]     chr1 1472601-1472650      * |         0
  [10]     chr1 1472651-1472750      * |         1
  [11]     chr1 1472751-1500000      * |         0
  -------
  seqinfo: 455 sequences from an unspecified genome

On Windows

> import("https://rlbase-data.s3.amazonaws.com/coverage/SRX7671349_hg38.bw", which = GRanges("chr1:1e6-1.5e6"))
Error in seqinfo(con) : UCSC library operation failed
In addition: Warning message:
In seqinfo(con) :
  Couldn't open https://rlbase-data.s3.amazonaws.com/coverage/SRX7671349_hg38.bw

ADD REPLY • link 3.2 years ago millerh1 ▴ 10

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Hi,

rtracklayer::import.bw() is supposed to work on Windows nowadays, but well, I see that I still avoid it on several pieces of derfinder at https://github.com/lcolladotor/derfinder/search?q=windows.

Lately though, I've been using megadepth since Christopher Wilks provides binaries for it that work on Windows (and other OS). See https://github.com/LieberInstitute/megadepth or the Bioconductor landing page for more information.

Best, Leo

ADD REPLY • link 3.2 years ago Leonardo Collado Torres ★ 1.1k

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Are you sure your filename does not have an extension, like .bw?

ADD REPLY • link 4.8 years ago Michael Lawrence ★ 11k