Question: Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading
0
gravatar for Denis
8 months ago by
Denis200
Denis200 wrote:

Hi,

I've executed the prefetch command of SRA toolkit which is in my case supposed to call the Aspera ascp command line utility internally. My command line was:

/home/sratoolkit.2.10.0-ubuntu64/bin/prefetch -a "/home/.aspera/connect/bin/ascp|/home/.aspera/connect/etc/asperaweb_id_dsa.openssh" -O /home/Data -X 100000000 SRR6856355

However, in the log file i got :

2020-03-18T11:15:00 prefetch.2.10.0: 1) Downloading 'SRR6856357'...
2020-03-18T11:15:00 prefetch.2.10.0: Downloading via https...
2020-03-18T12:51:32 prefetch.2.10.0: https download succeed

It's seems that, prefetch does not use the Aspera ascp.

How can i turn on Aspera ascp to speed up the process?

next-gen genome • 1.0k views
ADD COMMENTlink written 8 months ago by Denis200
4
gravatar for ATpoint
8 months ago by
ATpoint42k
Germany
ATpoint42k wrote:

SRA data can no longer be downloaded via Aspera, see https://github.com/ncbi/sra-tools/issues/255

ADD COMMENTlink modified 8 months ago • written 8 months ago by ATpoint42k

Thank you for sharing this information. Bad news.It's too slow via https. Any suggestion to accelerate the download?

ADD REPLYlink written 8 months ago by Wang10
1

No, just wait and have coffee :) Still, the file SRR6856357 is not overly large, should actually not take a long time. I could download it with prefetch in little less than two minutes. Maybe you have a slow internet connection or massive I/O bottlenecks.

Search for the file with https://sra-explorer.info/ and then try the download links it provides. Maybe some work better.

ADD REPLYlink written 8 months ago by ATpoint42k

Hi! That's interesting, as for me it takes almost 1 hour to download SRR6856357 with prefetch on HPC cluster.

ADD REPLYlink written 8 months ago by Denis200
1

Probably a bad connection then or massive I/O trouble, we had then when multiple file servers were malfunctioning long ago. I suggest you contact the admin for this.

ADD REPLYlink written 8 months ago by ATpoint42k

Thanks a lot. Will try to manage that.

ADD REPLYlink written 8 months ago by Denis200
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