Entering edit mode
4 months ago
Maryam • 0
Hello all, could you please help me, I can't download data from TCGA.
library(TCGAbiolinks) stadquery <- GDCquery(project = "TCGA-STAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts", legacy = F, experimental.strategy = "RNA-Seq") GDCdownload(query = stadquery, method = "api")
Unfortunately when I run GDCdownload I get this error:
Downloading: 260 MB At least one of the chunks download was not correct. We will retry Downloading chunk 1 of 2 (235 files, size = 998.900727 MB) as Mon_Jan_23_20_37_03_2023_0.tar.gz Downloading: 260 MB Error in GDCdownload.aux(server, manifest.aux, name.aux, path) : There was an error in the download process (we might had a connection problem with GDC server). Please run this function it again. Try using method = `client` or setting files.per.chunk to a small number.
I also tried "client" method but I get this error:
Downloading data for project TCGA-STAD trying URL '/files/public/file/gdc-client_v1.6.1_Windows_x64.zip' Error in download.file(url, ...) : cannot open URL '/files/public/file/gdc-client_v1.6.1_Windows_x64.zip' In addition: Warning message: In download.file(url, ...) : URL '/files/public/file/gdc-client_v1.6.1_Windows_x64.zip': status was 'URL using bad/illegal format or missing URL
I also tried files.per.chunk...
I really need the data and I don't know what to do. I would be grateful if you could help me.
Thanks in advance
I have the same issue!
I am using R4.2.3 on windows. I used the method you suggested, I have changed my internet connection and also I used vpn. but still I am getting these two errors.
GDCdownloaddidn't download the files completely
The function I'm using is: