dbGAP control data access download

Hi Everyone,

I am trying to get the TopMED data from dbGAP, where I have assigned as a downloader and I can see them in the SRA run selector as a list.

However, I have followed the below step to get the data using curl approach and I am not able to download the all the SRR files.

curl -s -X POST -F ngc="@prjv1_XXXXXX.ngc" "https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR000XXX&location=gs.us&filetype=cram"
{"version": "2","result": [{"bundle": "SRR000XXX","status": 404,"msg": "no data"}]}

Any help is highly appreciated.

Thank you, Abhishek

dbgap

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updated 6 months ago by Ram

• written 6 months ago by shrivastav.k.abhi •

Are you following a guide/set of instructions or is this a command line you created on your own?

While someone more knowledgeable about this will respond, the instructions from NCBI (SRA toolkit required) show this: https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbgap-download/#downloading-with-ngc-for-use-on-

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written 6 months ago by GenoMax

I emailed them my previous code where I was using sratool kit and projectxxx.ngc key to prefetch the data: prefetch --ngc prj_XXXXX.ngc --option-file SRR_Acc_List_clean.txt

but they said it will not work for the controlled data and share me this link to follow:

https://locate.ncbi.nlm.nih.gov/sdl/2/

But even this is failing.

Best wishes

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written 6 months ago by shrivastav.k.abhi •

Did NCBI support give you the following (from the link in original post)?

location=gs.us

Cloud locations are generally something like location=s3.us-east-1 as shown in the example in the link above.

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written 6 months ago by GenoMax

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