fastq- dump error
2
0
Entering edit mode
6.3 years ago
k.kathirvel93 ▴ 310

Hi Everyone,

When i was trying to Download SRA files from SRA db by using fastq-dump, i am getting this error.

2018-06-25T12:30:27 fastq-dump.2.9.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

Can anyone solve this...Thanks in advance

RNA-Seq software error sequence • 7.2k views
ADD COMMENT
2
Entering edit mode

Hello,

could you please provide the complete command you use?

Also please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

fin swimmer

ADD REPLY
0
Entering edit mode

Thank you finswimmer Here is the code.

./fastq-dump --split-3 SRR5591599
ADD REPLY
0
Entering edit mode

You can directly download that experiment from ENA, as already suggested by ATpoint

ADD REPLY
0
Entering edit mode

Are you trying to download/access restricted data?

ADD REPLY
0
Entering edit mode

Hi genomax

I am not trying for restricted one, its a free access data only.

ADD REPLY
0
Entering edit mode

In my experience, the fastest and the most secure (without connection interruptions) is to use prefetch with aspera, then convert sra files to fastq with fastq-dump. The whole thing saves a lot of time.

ADD REPLY
4
Entering edit mode
6.3 years ago
ATpoint 84k

Don't use fq-dump for download. Use prefetch to get the SRA file, then fastq-dump to convert to fastq. See here for details. Alternatively, use the European Nucleotide Archive to get fastq files directly.

ADD COMMENT
0
Entering edit mode

Hi, I am getting the error like this..... while trying prefetch..

2018-06-26T03:47:43 prefetch.2.9.0: KClientHttpOpen - verifying CA cert 
    2018-06-26T05:13:20 prefetch.2.9.0 int: transfer incomplete while reading file within network system module - 7r: Cannot KStreamRead
    2018-06-26T05:13:20 prefetch.2.9.0: 1) failed to download SRR5591599.
ADD REPLY
0
Entering edit mode

Did you figure out the issue? I am getting the same error with prefetch

ADD REPLY
0
Entering edit mode

It's a huge SRA file (29GB). Did you ever tried another smaller SRA record? I experienced network fails on my local PC for such a large file.

ADD REPLY
0
Entering edit mode
6.3 years ago
Michele Busby ★ 2.2k

I got this today too and it actually proceeded through to the whole download even though it had the error message. So maybe wait and see if it finishes? You can do an "ls" to see if it's still loading. If it gives you the stats at the end it's good.

ADD COMMENT

Login before adding your answer.

Traffic: 848 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