Why fasterq-dump --split-3 give me only one file for paired-end SRA accession?

Question

[TPOB]

Hello guys, I was trying to retrieve a bunch of paired-end sra run from ena to get fastq files directly, but as a paired-end data, ena showed one file but displayed also paired-end in the Library Layout field ena page for this accession.

So I decided to download data from ncbi instead. I used prefetch to download the raw sra file, and tried three split option as below. All of them just gave me one file. And they complained that half of the reads are of 0-length. Why? What should I do to get r1 and r2 from it?

Answer 1

[MohammadAlkadi]

It seems that the files were uploaded wrongly. You can check the reads online and there are no paired reads.

If you check the original format you can see the original files as in the picture. In conclusion, no problem with the software.

[TPOB]

Ok... Thank you for that, maybe I should reach the author to address the problem.