GDCdownload() does not work with recently updated splice junction data

[ryanhchung]

**Hi,

I'm opening this thread to ask you about the error from GDCdownload() function to download splice junction data.

My codes are as follows:**

Download splicing variants data

stad.junction <- GDCquery( project = "TCGA-STAD", legacy = FALSE, data.category = "Transcriptome Profiling", data.type = "Splice Junction Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts" ) GDCdownload(stad.junction)

and this produces the following error:

Downloading data for project TCGA-STAD GDCdownload will download 407 files. A total of 1.328210268 GB The total size of files is big. We will download files in chunks Downloading chunk 1 of 2 (306 files, size = 997.698629 MB) as Mon_Apr_11_09_55_16_2022_0.tar.gz |========================================================================================================================================================================| 100% /usr/bin/gtar: This does not look like a tar archive

gzip: stdin: not in gzip format /usr/bin/gtar: Child returned status 1 /usr/bin/gtar: Error is not recoverable: exiting now Download completed At least one of the chunks download was not correct. We will retry Downloading chunk 1 of 2 (306 files, size = 997.698629 MB) as Mon_Apr_11_09_55_16_2022_0.tar.gz |========================================================================================================================================================================| 100% /usr/bin/gtar: This does not look like a tar archive

gzip: stdin: not in gzip format /usr/bin/gtar: Child returned status 1 /usr/bin/gtar: Error is not recoverable: exiting now Download completed Error in if (ret == 1) break : argument is of length zero

Can you solve this issue? Thanks!

[tiagochst]

@ryanhchung Those are controlled files. Do you have a token to download it ?

[ryanhchung]

@tiagochst Thanks! I will check it out :)