Hello,
I'm downloading public data files from NCBI using (for example)
fastq-dump --split-files -F --bzip2 SRR2637659 > SRR2637659.out 2> SRR2637659.err
however, these commands crash every 6 runs or so, and download very very slowly. So far the only solution is to simply start again when fastq-dump
fails.
The problem is that after I leave work I cannot restart this, or when I'm sleeping. Is there any option or clever trick so I don't have to keep manually re-starting this every time fastq-dump
fails?
or even better yet, is there an option that for a given accession number, e.g. GSE88888, I can download all fastq associated with this data set? that would simply downloading greatly as well.
thanks
What's the error it's failing with? For downloading all at once, look at this answer.
Edit: Got beat to it, his solution is easier.