Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading
1
0
Entering edit mode
2.4 years ago
Denis ▴ 230

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?

genome next-gen • 2.9k views
ADD COMMENT
4
Entering edit mode
2.4 years ago
ATpoint 64k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

Thanks a lot. Will try to manage that.

ADD REPLY

Login before adding your answer.

Traffic: 1482 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6