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Question: TCGAbiolinks data download problem
0
gravatar for Fernando
19 months ago by
Fernando0
Cuba
Fernando0 wrote:

Hello I'm new with Bioconductor and microarray analysis. I am trying to download data with the function TCGAdownload, and first I had this error:

Error in curl::curl_download(input, tt, mode = "wb", quiet = !showProgress) : 
  Timeout was reached

Then, for what I have read (TCGAbiolinks data download error ; A: TCGAbiolinks FTP address ) it seems a problem with the FTP address. So, I replaced the "https" for "http" from

>TCGAdownload
function (data = NULL, path = ".", type = NULL, samples = NULL,
    force = FALSE)
{
    dir.create(path, showWarnings = FALSE, recursive = TRUE)
    root <- "https://tcga-data.nci.nih.gov"
    .....
}

with the command:

trace(TCGAdownload,quote(root <- "http://tcga-data.nci.nih.gov"),at=5)

and now there isn't any error, it stays frozen in the download step but without downloading anything:

trying URL 'http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/gbm/cgcc/unc.edu/agilentg4502a_07_2/transcriptome/unc.edu_GBM.AgilentG4502A_07_2.Level_1.2.0.0.tar.gz.md5'
Content type 'application/x-gzip' length 85 bytes
downloaded 85 bytes

can someone help me? Here are the codes:
 

library("TCGAbiolinks", lib.loc="C:/Program Files/R/R-3.2.4revised/library")
trace(TCGAdownload,quote(root <- "http://tcga-data.nci.nih.gov"),at=5)
query <- TCGAquery(tumor = "gbm", platform = "AgilentG4502A_07_2", level=1)
TCGAdownload(query,force=TRUE)
ADD COMMENTlink modified 19 months ago • written 19 months ago by Fernando0
1

Hi, 

the files for level 1 are 23 GB each folder. The download at least started? I'm running in linux and it is working for the moment.

> > > -=-=-=-=

| Downloading:4 folders

| Path:.

-=-=-=-=

  |                                                                      |   0%

Downloading:unc.edu_GBM.AgilentG4502A_07_2.Level_1.2.0.0.tar.gz

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100    85  100    85    0     0     68      0  0:00:01  0:00:01 --:--:--    68

 

Also it might be a windows problem or the server was down when TCGAbiolinks tried to download from TCGA server. Do you have the same problem if you try to download only one sample?

 

Best regards,

Tiago

ADD REPLYlink written 19 months ago by tiagochst90

Thank for your answer, it must be that. I tried later to download another archives of level 2 and there wasn't any problem.

ADD REPLYlink written 18 months ago by Fernando0
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