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GDCdownload error: 'No such file or directory' #618

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Mincana-Huang opened this issue Feb 17, 2024 · 1 comment
Open

GDCdownload error: 'No such file or directory' #618

Mincana-Huang opened this issue Feb 17, 2024 · 1 comment

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@Mincana-Huang
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GDCdownload(query_col_wxs, directory = "TCGA_DATA_DL")
Downloading data for project TCGA-COAD
GDCdownload will download 457 files. A total of 82.8324 MB
Downloading as: Sat_Feb_17_21_15_58_2024.tar.gz
Downloading: 83 MB <simpleWarning in file.create(to[okay]): cannot create file 'TCGA_DATA_DL/TCGA-COAD/Simple_Nucleotide_Variation/Masked_Somatic_Mutation/61132188-579f-4baa-891f-9c9b2b3fae1f/e37894df-0715-4171-bb88-0b175dccee7f.wxs.aliquot_ensemble_masked.maf.gz', reason 'No such file or directory'>

The same error occurred in the remaining 400+ files. I checked to make sure the directory exists and ran RStudio as administrator.
Then I used the client method to download, and the error message was as follows.
Downloading data for project TCGA-COAD
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'

@dstewar6
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Hi Mincana-Huang, I am currently having the same issue when I try to use method = "client", were you ever able to find a solution to this? Thanks!

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