Problem Downloading Clinical Data

[kvougas]

When I ran the following: query <- GDCquery(project = "TCGA-OV", data.category = "Clinical") GDCdownload(query,directory = "~/Projects/GDC/Clinical")

I got the following error:

**Accessing GDC. This might take a while... GDCdownload will download: 31.370846 MB compressed in a tar.gz file Downloading as: Mon_Aug_22_09_22_25_2016.tar.gz |======================================================================================| 100% /bin/tar: This does not look like a tar archive

gzip: stdin: not in gzip format /bin/tar: Child returned status 1 /bin/tar: Error is not recoverable: exiting now [1] 2 Error in GDCdownload(query, directory = "~/Projects/GDC/Clinical") : There was an error in the download process, please execute it again In addition: Warning message: In untar(name) : ‘/bin/tar -xf 'Mon_Aug_22_09_22_25_2016.tar.gz'’ returned error code 2**

The same error is also generated with: "TCGA-LGG" & "TCGA-LIHC"

[tiagochst]

Hi,

I was able to run the code, could you send me your sessionInfo(), also, could you try to run query <- GDCquery(project = "TCGA-OV", data.category = "Clinical") GDCdownload(query) Maybe it is related to the ~, but it is working in linux.

[kvougas]

I also ran it under Ubuntu 16.04LTS. I think it was a glitch with the GDC. Now I reran it, everything was fine.

Thanks

[huwenhuo]

I know this is closed. But I got the same problem and solved by GDCdownload(query, method = 'api') I hope this is helpful for someone.

[TBradley27]

Hello,

I am afraid that this is still an issue, and all of the recommendations in this thread do not successfully resolve this issue.

I have tested this on R version 4.3.1 with TCGAbiolinks version 2.30.0

I am receiving the same/similar error messages to the OP

Can I request please that this issue is reopened?

[TBradley27]

Hello again,

With more investigation, I discovered that this issue is due to users attempting to download of controlled data without using a token i.e. using GDCdownload with the token.file parameter being empty. The result is that a file is downloaded into the user's directory with the file extension .tar.gz which is not actually a compressed archive file.

Despite the file extension, this is actually a plain text file with the following contents:

{"message":"Your token is invalid or expired. Please get a new token from GDC Data Portal."}

To prevent confusion, I believe that there is a better method of catching/managing this error, and informing users of the true cause of the problem