This is a test version of Biostars. For the public version, visit https://www.biostars.org.
problem in fastq-dump of SRA file

I have downloaded an SRA file and named it "fastq.sra". Then I used fastq-dump as

fastq-dump fastq.sra --split-3 -I

BUt following error is shown

err: item not found while constructing within virtual database module - the path 'fastq.sra' cannot be opened as database or table

sra fastq-dump
• 3,755 views • link
updated by jomo018 jomo018 • written by majeedaasim • majeedaasim

When possible search EBI-ENA with your SRA# and directly download fastq files avoiding all such issues.

• 0 views • link
written by GenoMax GenoMax

3 answers

How did you download the file? It’s likely that you’ve downloaded something like an error page. The first 8 bytes of the file should be ‘NCBI.sra’ (see here) which you can confirm by dumping the ASCII strings in the file:

$ strings fastq.sra | head -n1
NCBI.sra
• 0 views • link
written by Matt Shirley Matt Shirley

I think you should use the correct path for the command like this: 

 /path/fastq-dump --split-3 file.sra
• 0 views • link
written by Ram Ram

Include the path of fastq.sra. For example:

fastq-dump ./fastq.sra --split-3 -I
• 0 views • link
written by jomo018 jomo018

Log in to answer this question.

More posts like this