fastq dump

Question

[sehriban.buyukkilic]

hi everyone, Im trying to do split fastq files for paired read, but it's giving error. I tried a lot of way unfortunately didn't work. I need help for this problem.

2022-12-30T18:24:36 fastq-dump.3.0.1 err: item not found while constructing within virtual database module - the path 'SRR1170924.fastq' cannot be opened as database or table fastq-dump quit with error code 3

[ATpoint]

What is your command line?

[sehriban.buyukkilic]

/truba/home/sbuyukkilic/fastqc_tool/sratoolkit.3.0.1-centos_linux64/bin/fastq-dump --split-3 SRR1170924.fastq

this command ı'm running

[barslmn]

Take a look at his thread How to split paired end SRA file into 2 correct fastq files

[sehriban.buyukkilic]

thank you so much, I did it. But my problem didn't solved.

Answer 1

[ATpoint]

The command must be without .fastq, though it would be easier to use sra-explorer.info and get fastq download links directly from the web service.

Answer 2

[GenoMax]

This does not appear to be a paired-end dataset. However if you look in Data access tab (LINK) the originally submitted files seems to be in *.txt.gz format (and there are three) so the mystery deepens. You could try to download those files from AWS and see what you get.