Error in GDC download in TCGAbiolinks
Entering edit mode
14 days ago
Maryam • 0

Hello all, could you please help me, I can't download data from TCGA.


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/'
Error in download.file(url, ...) : 

  cannot open URL '/files/public/file/'

In addition: Warning message:

In download.file(url, ...) :
URL '/files/public/file/': 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.

GDCdownload TCGAbiolinks R • 224 views
Entering edit mode
13 days ago

try GDCdownload(query = stadquery, method = "api", files.per.chunk = 1) and try to conect internet by ethernet cable

This worked for me Good Luck :)


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