Question: fastq-dump timeout exhausted error
0
gravatar for bxia
3.2 years ago by
bxia150
bxia150 wrote:

Hi, I got this error message from fastq-dump:

fastq-dump.2.8.0 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

but I have SRA downloaded in the local folder. I wonder whether I can ignore this error message

sra • 6.6k views
ADD COMMENTlink modified 2.8 years ago by samesense40 • written 3.2 years ago by bxia150

What was your fastq-dump command line?

Also posting the error as a title of the post is never informative. You could just say fastq-dump error to keep the title streamlined.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by genomax85k

fastq-dump --split-3 SRR998480

I am wondering whether it is really using the local downloaded SRA

ADD REPLYlink written 3.2 years ago by bxia150
1

What does --split-3 do?

ADD REPLYlink written 12 months ago by O.rka180
2
gravatar for genomax
3.2 years ago by
genomax85k
United States
genomax85k wrote:

How about explicitly doing fastq-dump --split-3 /path_to/SRR998480.sra

ADD COMMENTlink written 3.2 years ago by genomax85k

ok, I see, that will make sense

Thanks

ADD REPLYlink written 3.2 years ago by bxia150
1
gravatar for samesense
2.8 years ago by
samesense40
United States
samesense40 wrote:

NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as sra-tools, ncbi-vdb or ngs.

If you develop software that relies on sra-tools, ncbi-vdb or ngs in any way, you will likely need to update your code so that it accesses NCBI using HTTPS.

More here: https://github.com/ncbi/sra-tools

So much for reproducible research.

ADD COMMENTlink written 2.8 years ago by samesense40

Wait... how does this affect when I just need to download a SRA record using fastq-dump w/ my current version?

ADD REPLYlink written 12 months ago by O.rka180
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