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