Caveats
- A good internet connection is required. Retrieving
fastq can be really slow and is thus a bottleneck.
fasterq-dump will randomly segfault.
At first we thought this was caused by connection problems, but running ping ruled this out. Apparently, the segfault is a known issue.- The workflow will inevitably fail if you try building the genome’s index on a machine with less than ~30 GB of RAM available.
- As a general rule, tweak all parameters to reasonable values that fit your setup and needs. We don’t know your hardware, you do ;)