problem in fastq-dump of SRA file

Question

[majeedaasim]

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

[GenoMax]

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

Answer 1

[Matt Shirley]

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

Answer 2

[Ram]

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

 /path/fastq-dump --split-3 file.sra

Answer 3

[jomo018]

Include the path of fastq.sra. For example:

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