convert SRA to fastq

Question

[mo.ghasemi717]

Hi everyone

Recently I download some SRA files (12 files) using this command from NCBI:

prefetch ERR4172779

all of SRA file were dowloaded properly but when I try to convert them to fastq files using this command :

fastq-dump --split-3  ERR4172779

it shows this:

2020-08-12T11:42:02 fastq-dump.2.9.4 err: file invalid while opening directory within file system module - failed to resolve column 'READ' idx '1'
2020-08-12T11:42:02 fastq-dump.2.9.4 err: file invalid while opening directory within file system module - failed to resolve column 'READ' idx '1'
2020-08-12T11:42:02 fastq-dump.2.9.4 err: file invalid while opening directory within file system module - failed ERR4172779.sra
==================================================
An error occurred during processing.
A report was generated into the file '/home/mohammad/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to '[e-mail]' for assistance.

What's the problem?

[lieven.sterck]

Hello mo.ghasemi717,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[lieven.sterck]

a tool I found very helpful for retrieving data is the following:

https://sra-explorer.info/

it says SRA, but you can also get download links for ENA (and I second dariober post below to use ENA rahter than SRA for this)

Answer 1

[dariober]

Looking at the ENA archive here, it seems fastq files are not available for this accession. However, they provide BAM files.

(As a side note, in my opinion is better to work with ENA than SRA, see also this answer of mine at https://bioinformatics.stackexchange.com/a/14121/339)

[mo.ghasemi717]

thank you dear dariober for your explanation