Question: problem in fastq-dump of SRA file
0
gravatar for majeedaasim
2.1 years ago by
majeedaasim40
United States
majeedaasim40 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 • 1.4k views
ADD COMMENTlink modified 2.1 years ago by jomo018520 • written 2.1 years ago by majeedaasim40

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

ADD REPLYlink written 2.1 years ago by genomax76k
1
gravatar for Matt Shirley
2.1 years ago by
Matt Shirley9.2k
Cambridge, MA
Matt Shirley9.2k 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 2.1 years ago by Matt Shirley9.2k
0
gravatar for Ram
2.1 years ago by
Ram130
Germany
Ram130 wrote:

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

 /path/fastq-dump --split-3 file.sra
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Ram130
0
gravatar for jomo018
2.1 years ago by
jomo018520
jomo018520 wrote:

Include the path of fastq.sra. For example:

fastq-dump ./fastq.sra --split-3 -I
ADD COMMENTlink written 2.1 years ago by jomo018520
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1831 users visited in the last hour