Issue downloading SRA files from NCBI

IFB Core Cluster Support IFB Core Cluster
1

Hello,

In the context of my PhD project, I'm working with publicly available scRNA-seq datasets. I need to download SRA files from NCBI in order to extract the fastq files and process them. I use the wget command to do this:

wget https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR8262952/SRR8262952.1

However, whenever I try to dowload a file specifically from NCBI it is rejected with a 403 forbidden error.

--2022-03-25 08:55:20-- https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR8262952/SRR8262952.1
Resolving sra-downloadb.st-va.ncbi.nlm.nih.gov... 165.112.9.238, 165.112.9.239, 165.112.9.237
Connecting to sra-downloadb.st-va.ncbi.nlm.nih.gov|165.112.9.238|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2022-03-25 08:55:21 ERROR 403: Forbidden.

Are we not allowed to download from NCBI using the IFB cluster? Would it be possible to take a look at this because so far I've been unable to download the files that I need?

Thank you!

Best,
Jessica

2

Bonjour Jessica,
It seems that your url is not accessible.
If you search for the run SRR8262952, you will find the page : https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8262952
In the tab "data access", we find the url allowing to access the data: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR8262952/SRR8262952.1
I hope this will help you.
Loraine

3

Hi,

I apologise for the late reply!
Thank you for your feedback, yes it seems I was using an older URL that is no longer available. I'll have to be more careful about that in the future.

Best,
Jessica