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
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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.
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.
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What was your
fastq-dumpcommand line?Also posting the error as a title of the post is never informative. You could just say
fastq-dumperror to keep the title streamlined.fastq-dump --split-3 SRR998480
I am wondering whether it is really using the local downloaded SRA
What does --split-3 do?
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.