prefetch download speed

Question

[Kiwi@ch]

Hi, I am currently trying to download multiple SRA repositories and for this installed sra-toolkit and I use the prefetch SRRs command. I am however facing reeeeeally slow download speed (in the order of 100ko/s to 1mo/s). I checked with my IT support and the the limitation is not coming from my side.

prefetch SRR12118334

2022-11-16T09:27:32 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-11-16T09:27:32 prefetch.3.0.0: 1) Downloading 'SRR12118334'...
2022-11-16T09:27:32 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-11-16T09:27:32 prefetch.3.0.0:  Downloading via HTTPS...

Alternatively using wget with direct ftp link does not work better.

I feel this is not the normal DL speed, and wonder what could be wrong and how to get files faster ? Thx

Answer 1

[ATpoint]

There is no need to go the path using sra-toolkit. You can enter your accessions at sra-explorer.info and get download links for fastq files directly.

sra-explorer : find SRA and FastQ download URLs in a couple of clicks

[Kiwi@ch]

Yes thx, I tried through the sra-explorer website (and also tried aspera installation and links) but end up with same extra slow download... (which is why I feel smthg must be problematic on my side).

[ATpoint]

It's also death slow for me. Probably some server issues at their side.

[GenoMax]

It took perhaps 15 sec to prefetch the SRR# above. Looks like a 653M file. Worth trying again.

[Kiwi@ch]

Damn... I am retrying and I am downloading at 232KiB/s... How to diagnose from where the slowliness is originating ?

EDIT: the problem was solved by itself, same cmd line last friday produced a +16Mo/s download...