Hi,
I have downloaded sra file from NCBI, SRR4242282.sra and I got three fastq files after use fastq-dump to extract fastq files from sra files. 
command :fastq-dump --split-3 --gzip SRR4242282.sra 
I have no idea with this result, I haven't met this before. Any suggestion would be appreciated. 

Please see my previous [post][1]: this is due to the fact that BOTH paired and unpaired reads are included in these sra files. Using the `--split-files` option does not work since this would lead to fastq-files that are incomplete. What you did is correct; simply use the files ending with `_1` and `_2` will do. The remaining files contains the unpaired reads, and can be trashed.


  [1]: https://www.biostars.org/p/185429/