sratoolkit prefetch command returns no result

Question

[AB]

Hi everyone,

I recently updated my sratoolkit from version 2.8 to 2.10.8. Now my prefetch command doesn't seem to be working.

I tried this prefetch -p SRR8387813 -o ~/SRAfiles/sra. It runs for some 5-10 mins. No progress messages despite the -p argument. No error messages. But then the file doesn't get downloaded either. Anyone else encountered something similar ? How do I solve this ?

Thanks

[GenoMax]

That looks like a 10x run but there is no original data submitted (look at the record in SRA under Data Access tab). You may be able to get three files by dumping reads out with --split-files.

Others have been having issues trying to retrieve 10x data from SRA recently. NCBI's 10x data management is a bit of mess or so it appears.

[AB]

That is just an example. I have the issue for any SRA file i try to download using prefetch. It works fine when I run it on my local directory. But what I really want to do is to use it to download the files to a remote server that has sratoolkit installed. fast-dump works on it. Just not prefetch.

Answer 1

[AB]

Turns out the server doesn't have an outbound network access. My bad. Sorry. Will have to do it locally.