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4 months ago
Kiwi@ch • 0

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: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.


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

prefetch srr fastq sra-toolkit sra • 527 views
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4 months ago
ATpoint 70k

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

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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).

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

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

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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...