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GDC portal data download

Hello

I'm trying to download some TCGA WXS data from GDC portal using gdc-client, but it's not working.

It just shows the error message like below even though I use new token.

ERROR: Unable to download 9bb44eab-cf7f-4335-ba58-1fe8e815f4a8: 403 Client Error: FORBIDDEN:     { "message": "Your token is invalid or expired. Please get a new token from GDC Data Portal." }
SUMMARY: Failed to download: 1
ERROR: 9bb44eab-cf7f-4335-ba58-1fe8e815f4a8: 403 Client Error: FORBIDDEN: {   "message": "Your token is invalid or expired. Please get a new token from GDC Data Portal." }

and my bash file for running the gdc-client is like this.

$path_gdc-client  download -t $token 9bb44eab-cf7f-4335-ba58-1fe8e815f4a8

What is the problem and how can I fix it?

gdc gdcportal tcga
• 6,878 views • link
updated by Ram Ram • written by a01039012387 • a01039012387

Do you have approved access for the TCGA controlled-access data?; Why not just try to directly specify the token instead of via a variable?; if you already have approved access, then you should be aware that the token expires relatively quickly, so, you have to download new ones after a month or so.

• 0 views • link
written by Kevin Blighe Kevin Blighe

I have approved access and download a new token just before running the command but it still not working.

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written by a01039012387 • a01039012387

At the risk of sounding completely condescending, this same command worked previously? - I never previously had to specify the -s parameter. How did you obtain the ID (9bb44eab-cf7f-4335-ba58-1fe8e815f4a8) for download? - I usually obtain a file manifest.

• 0 views • link
written by Kevin Blighe Kevin Blighe

1 answer

I put the -s parameter since the GDC url was changed and it worked. And as your comment, I reobtain the ID from a file manifest and It's working! I seem to have made a mistake while getting the ID. I do not know why the error message says the token is a problem, though. Thank you so much for your help=3

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written by a01039012387 • a01039012387

Okay - cool! Glad that it now works.

• 0 views • link
written by Kevin Blighe Kevin Blighe

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