R getting "stuck" with RoadMap resource retrieval through AnnotationHub
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@vanesa_1230-12951
Last seen 4.6 years ago

Greetings!

I'm having a hard time trying to retrieve RoadMap resources using AnnotationHub (e.g.  ah[['AH49441']] ). The download does reach a 100%, but then the process will never exit. I don't get any error message, but I left this overnight to see if it would eventually end the process but it just didn´t happen. Is there anything going on with the server? Thanks in advance

roadmap project annotationhub • 787 views
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@james-w-macdonald-5106
Last seen 9 days ago
United States

Seems to work for me. Maybe try again?

> hub <- AnnotationHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2017-04-24
> z <- hub[["AH49441"]]
require("rtracklayer")
downloading from 'https://annotationhub.bioconductor.org/fetch/56161'
retrieving 1 resource
  |======================================================================| 100%
> z
BigWigFile object
resource: C:/Users/jmacdon/AppData/Roaming/AppData/.AnnotationHub/56161
> mcols(hub)["AH49441",]
DataFrame with 1 row and 15 columns
                                         title   dataprovider      species
                                   <character>    <character>  <character>
AH49441 E002_RRBS_FractionalMethylation.bigwig BroadInstitute Homo sapiens

> import(z)
GRanges object with 3878598 ranges and 1 metadata column:
            seqnames               ranges strand |             score
               <Rle>            <IRanges>  <Rle> |         <numeric>
        [1]     chr1       [10497, 10497]      * | 0.970000028610229
        [2]     chr1       [10498, 10498]      * | 0.970000028610229
        [3]     chr1       [10525, 10525]      * | 0.970000028610229
        [4]     chr1       [10526, 10526]      * | 0.970000028610229
        [5]     chr1       [10542, 10542]      * |              0.75
        ...      ...                  ...    ... .               ...
  [3878594]     chrY [59033065, 59033065]      * | 0.699999988079071
  [3878595]     chrY [59033091, 59033091]      * | 0.280000001192093
  [3878596]     chrY [59033092, 59033092]      * | 0.280000001192093
  [3878597]     chrY [59033101, 59033101]      * | 0.230000004172325
  [3878598]     chrY [59033102, 59033102]      * | 0.230000004172325
  -------
  seqinfo: 24 sequences from an unspecified genome
>
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shepherl 2.9k
@lshep
Last seen 51 minutes ago
United States

I also cannot reproduce the problem.  Could you please provide the exact code you ran as well as the results of sessionInfo(). 

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Thank you for your answers. I have now been able to retrieve 3 different resourses at most before R or RStudio gets "stuck". I actually have to terminate R since it wouldn't allow me to manually stop the process. I'm not sure if the data set I'm trying to retrieve could be too large or there's something going on with the internet connection. This is the code I'm using:

> ah <- AnnotationHub()

snapshotDate(): 2016-10-11

>

> #SUBSET BROAD INSTITUTE DATA

> epiRoad <- subset(ah, species=="Homo sapiens" & dataprovider=="BroadInstitute")

>

> #SELECT CONSOLIDATED GENOMES

> epiRoad_consolidated <- query(epiRoad, c("E{1}[0-9]{3}[^0-9]", "EID_metadata"), pattern.op=`|`)

>

> #SELECT H3K4ME1 NARROW PEAKS

> narrow.h3k4me1 <- query(epiRoad_consolidated, c("h3k4me1", "narrow ChIP-seq"))

>

> data.narrow.h3k4me1 <- lapply(X = names(narrow.h3k4me1), FUN = function(x){epiRoad_consolidated[[x]]})

require(“rtracklayer”)

downloading from ‘https://annotationhub.bioconductor.org/fetch/35299’

retrieving 1 resource

  |==============================================================================| 100%

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I'm still having trouble reproducing as I can run your code above with no issues.  What is your output of sessionInfo()? We want to make sure you are using the most updated versions of all the packages for your version of R, you can check by using biocLite().  From the look of the snapshot date of AnnotationHub, I would guess that you are running an older version of R and AnnotationHub;  I would suggest if you continue to have issues to update to the most current release. Also, you might consider checking your system's memory to make sure you have enough space to download.  

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I really appreciate all your collaboration. I believe that I finally found out that the issue was the network connection...I feel so ashamed. Eventhough some packages are not the most updated version, the code is being running today successfully without the need of making any update. Today's data transfer rate is still low, but at least it's allowing me to do the download. Sorry for the inconvenience; I didn't check this yesterday since I didn't really believe it could be that bad. Many thanks!!!

 

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No problem.  We've all dealt with slow network issues.  Feel free to post more if you find you are having any other issues. 

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