Hi, I am downloading raw RNA-seq data from SRA using fastq-dump from the SRA toolkit. I am using the --split-3 option, so that when it is single-end, I get a single fastq file per sample, and two fastq files if paired-end. It seems to be working fine, except that for a few runs from paired-end experiments, I am getting a single fastq file instead of two. An example is for the GSE75440 dataset, for sample GFP rep2 and GFP rep3 (SRR2969254 and SRR2969255). What could explain this behaviour? Thank you.
EDIT: One thing I should add is that when running fastq-dump, I get the following error:
Rejected 52180955 READS because of filtering out non-biological READS Read 52180955 spots for SRR2969254.sra Written 52180955 spots for SRR2969254.sra
Is the single fastq file produced usable?