Error with SRA Toolkit prefetch command
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Entering edit mode
5 months ago
elisheva ▴ 110

Hi!
I am trying to download several files using the prefetch command of SRA Toolkit:

prefetch -v SRR5461433

But I keep getting the following error:

libs/kns/http-client.c:1570:KClientHttpStreamTimedRead: transfer incomplete while reading file within network system module - Cannot KStreamRead: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5461433/SRR5461433.1
2021-05-19T08:43:33 prefetch.2.9.3: 1) failed to download SRR5461433

I tried to google for several solutions, but couldn't find anything helpful.
Does anyone know how to fix this problem?
TIA.

timeout sra ncbi https • 180 views
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2
Entering edit mode
5 months ago
ATpoint 55k

One of these cryptic sra-toolkit errors. You can directly get a download link for the fastq file from sra-explorer.info, see also sra-explorer : find SRA and FastQ download URLs in a couple of clicks

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