Question: problem in fastq-dump of SRA file
0
gravatar for majeedaasim
2.9 years ago by
majeedaasim50
United States
majeedaasim50 wrote:

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

fastq-dump sra • 1.7k views
ADD COMMENTlink modified 2.9 years ago by jomo018610 • written 2.9 years ago by majeedaasim50

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

ADD REPLYlink written 2.9 years ago by GenoMax92k
1
gravatar for Matt Shirley
2.9 years ago by
Matt Shirley9.4k
Cambridge, MA
Matt Shirley9.4k wrote:

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
ADD COMMENTlink written 2.9 years ago by Matt Shirley9.4k
0
gravatar for Ram
2.9 years ago by
Ram150
Germany
Ram150 wrote:

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

 /path/fastq-dump --split-3 file.sra
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ram150
0
gravatar for jomo018
2.9 years ago by
jomo018610
jomo018610 wrote:

Include the path of fastq.sra. For example:

fastq-dump ./fastq.sra --split-3 -I
ADD COMMENTlink written 2.9 years ago by jomo018610
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