fastq-dump timeout exhausted error

Question

[bxia]

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

[GenoMax]

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.

[bxia]

fastq-dump --split-3 SRR998480

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

[O.rka]

What does --split-3 do?

[Akanksha]

Legacy 3-file splitting for mate-pairs: First biological reads satisfying dumping conditions are placed in files _1.fastq and _2.fastq If only one biological read is present it is placed in *.fastq Biological reads and above are ignored.

Answer 1

[GenoMax]

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

[bxia]

ok, I see, that will make sense

Thanks

[Akanksha]

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 ) same error encountered just dont know if its a warning or an error, an dif its a warning then should i stop the run.

Answer 2

[samesense]

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.

[O.rka]

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