Question

SRA Toolkit fastq-dump error

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7.0 years ago

pratibha_jagannatha ▴ 20

I'm getting this error when using fastq-dump in the SRA toolkit and am not sure what it means or how to fix it...

fastq-dump.2.8.2 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

RNA-Seq • 4.8k views

ADD COMMENT • link updated 4.8 years ago by nc52 ▴ 10 • written 7.0 years ago by pratibha_jagannatha ▴ 20

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Did you ever get an answer to this? I am having the same problem.

ADD REPLY • link 4.8 years ago by nc52 ▴ 10

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Have you looked to see if there are any local firewall restrictions?

ADD REPLY • link 4.8 years ago by GenoMax 141k

score 2 · Answer 1 · 2017-04-23

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7.0 years ago

GenoMax 141k

If you are looking for a specific SRA# it may be easier to get the fastq files directly from EBI-ENA. Just search with that accession.

ADD COMMENT • link 7.0 years ago by GenoMax 141k

score 1 · Answer 2 · 2019-07-11

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4.8 years ago

ATpoint 81k

Do yourself a favor and download files directly from the ENA, see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD COMMENT • link 4.8 years ago by ATpoint 81k