Question: SRA prefetch error
0
gravatar for kousi31
23 months ago by
kousi3130
kousi3130 wrote:

I am using sratoolkit.2.9.2.ubuntu64. I tried downloading RNA-seq data with the command prefetch ERR315616. (eukaryote data)

I got the error message

2018-12-17T05:51:35 prefetch.2.8.2 sys: libs/kns/unix/syssock.c:606:KSocketTimedRead: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
2018-12-17T05:51:35 prefetch.2.8.2 int: libs/kns/unix/syssock.c:606:KSocketTimedRead: timeout exhausted while reading file within network system module - �
2018-12-17T05:51:35 prefetch.2.8.2: 1) failed to download ERR315616.

But I am able to download influenza genome with the same command prefetch SRR8292123.

Please help and thanks in advance.

software error • 2.3k views
ADD COMMENTlink modified 23 months ago by rrbutleriii80 • written 23 months ago by kousi3130

For me it worked (with sra toolkit 2.8.2):

prefetch ERR315616

2018-12-17T12:11:52 prefetch.2.8.2: 1) Downloading 'ERR315616'...
2018-12-17T12:11:52 prefetch.2.8.2:  Downloading via https...
2018-12-17T12:20:09 prefetch.2.8.2: 1) 'ERR315616' was downloaded successfully

So my guess is that something is not installed or not working properly on your machine.

ADD REPLYlink modified 23 months ago • written 23 months ago by Benn8.0k
1
gravatar for ATpoint
23 months ago by
ATpoint42k
Germany
ATpoint42k wrote:

The data are backed up at the European Nucleotide Archive (ENA). You can get them from there in fastq format. For batch downloads, also see my tutorial Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA).

ADD COMMENTlink written 23 months ago by ATpoint42k
0
gravatar for rrbutleriii
23 months ago by
rrbutleriii80
US, Chicago
rrbutleriii80 wrote:

This may be a temporary system outage, see: https://github.com/ncbi/sra-tools/issues/84.

Otherwise, based on the timeout and failed SSL handshake I wouls suspect a firewall connection issue. Do you normally connect via a proxy on your network?

ADD COMMENTlink written 23 months ago by rrbutleriii80
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