SRA Toolkit cannot download

Question

[Barış Ekim]

Hello,

I'm new to the SRA toolkit, and I'm trying to download SRR8959110 via prefetch on a MacOS 10.14.4 Mojave. I'm getting the following errors:

2019-06-16T18:00:06 prefetch.2.9.3 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

2019-06-16T18:00:06 prefetch.2.9.3 int: timeout exhausted while reading file within network system module - Cannot KStreamRead: https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/008749/SRR8959110

2019-06-16T18:00:06 prefetch.2.9.3: 1) failed to download SRR8959110

I doubt it's anything on SRA's end and probably a firewall issue, but I couldn't find anything anywhere else. Any suggestions?

Answer 1

[Philipp Bayer]

You can setup prefetch to use ascp, which uses a different download system than the regular http-based one, and is way faster, and usually doesn't time out (on me!).

You'll have to setup ascp first and then use one extra flag in prefetch, see this tutorial: https://edwards.sdsu.edu/research/aspera-fastq-dump-and-prefetch/

[ATpoint]

Download via prefetch followed by parallel-fatq-dump is also covered in the tutorial below after installing Aspera.

Answer 2

[ATpoint]

Get data directly as fastq from the ENA, see my tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)

[Barış Ekim]

Wasn’t aware of this, thanks!