fastq- dump error

Question

[k.kathirvel93]

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

[finswimmer]

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.

fin swimmer

[k.kathirvel93]

Thank you finswimmer Here is the code.

./fastq-dump --split-3 SRR5591599

[WouterDeCoster]

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

[GenoMax]

Are you trying to download/access restricted data?

[k.kathirvel93]

Hi genomax

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

[grant.hovhannisyan]

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.

Answer 1

[ATpoint]

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.

[k.kathirvel93]

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.

[JJDollar]

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

[wm]

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.

Answer 2

[Michele Busby]

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.