Hello, I have tried to download TCGA-OV RNA-seq data by GDCdownload() with different "files.per.chunk" for several times, but the same error still occurred.
Here are the code & error:
#code1
query1 = GDCquery(project = "TCGA-OV",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts")
##error
(part of the log msg)
Downloading: 11 MB Downloading chunk 38 of 39 (10 files, size = 42.43942 MB) as Wed_Nov9_10_51_51_2022_37.tar.gz
Downloading: 11 MB Downloading chunk 39 of 39 (1 files, size = 4.260786 MB) as Wed_Nov9_10_51_51_2022_38.tar.gz
|=======| 100%
At least one of the chunks download was not correct. We will retry
Of the 381 files for download 380 already exist.
We will download only those that are missing ones.
Downloading chunk 1 of 1 (1 files, size = 4.260786 MB) as Wed_Nov__9_10_51_51_2022_0.tar.gz
|=======| 100%
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 think the last filename may differ from the previous version )
#code 3
(Then I modified the 'GDCdownload' code, )
GDCdownload(query = query1, directory = "data",method = 'client')
##error
Error in if (grepl("^https?://", url))
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
And my TCGAbiolink version is 2.22.4.
Hello, I have tried to download TCGA-OV RNA-seq data by GDCdownload() with different "files.per.chunk" for several times, but the same error still occurred.
Here are the code & error: #code1 query1 = GDCquery(project = "TCGA-OV", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts")
#code 2 GDCdownload(query = query1, directory = "data", files.per.chunk = 10)
##error (part of the log msg) Downloading: 11 MB Downloading chunk 38 of 39 (10 files, size = 42.43942 MB) as Wed_Nov9_10_51_51_2022_37.tar.gz Downloading: 11 MB Downloading chunk 39 of 39 (1 files, size = 4.260786 MB) as Wed_Nov9_10_51_51_2022_38.tar.gz |=======| 100% At least one of the chunks download was not correct. We will retry Of the 381 files for download 380 already exist. We will download only those that are missing ones. Downloading chunk 1 of 1 (1 files, size = 4.260786 MB) as Wed_Nov__9_10_51_51_2022_0.tar.gz |=======| 100% 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 =
clientor setting files.per.chunk to a small number. (I think the last filename may differ from the previous version )#code 3 (Then I modified the 'GDCdownload' code, ) GDCdownload(query = query1, directory = "data",method = 'client')
##error Error in if (grepl("^https?://", url))
sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) And my TCGAbiolink version is 2.22.4.
Looking forward to your reply!
THANKS!