Question: SRA prefetch error
0
gravatar for kousi31
6 months ago by
kousi310
kousi310 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 • 469 views
ADD COMMENTlink modified 6 months ago by rrbutleriii60 • written 6 months ago by kousi310

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 6 months ago • written 6 months ago by Benn6.9k
1
gravatar for ATpoint
6 months ago by
ATpoint18k
Germany
ATpoint18k 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 6 months ago by ATpoint18k
0
gravatar for rrbutleriii
6 months ago by
rrbutleriii60
US, Chicago
rrbutleriii60 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 6 months ago by rrbutleriii60
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