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fastq- dump error

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
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updated by Michele Busby Michele Busby • written by k.kathirvel93 k.kathirvel93

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

• 1 views • link
written by finswimmer finswimmer

Thank you finswimmer Here is the code.

./fastq-dump --split-3 SRR5591599
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written by k.kathirvel93 k.kathirvel93

Are you trying to download/access restricted data?

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written by GenoMax GenoMax

Hi genomax

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

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written by k.kathirvel93 k.kathirvel93

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.

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written by grant.hovhannisyan grant.hovhannisyan

2 answers

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.

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written by ATpoint ATpoint

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.
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written by k.kathirvel93 k.kathirvel93

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

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written by JJDollar • JJDollar

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.

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written by wm wm

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.

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written by Michele Busby Michele Busby

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