I am a bit confused now. In the link you provided they recommend quality filtering before starting dada 2. Yet, I can find other posts, where quality filtering prior to DADA2 is not recommended: DADA2 and quality filtering?
The dada2 workflow in QIIME 2 performs quality filtering as an initial step so earlier filtering is unnecessary. It probably would not hurt, but would be redundant. Hence the mixed messages in different forum posts.
That link seems to describe the dada2 workflow that is already implemented in QIIME 2.
return code -9 is a memory error — the best fix is to find a more powerful machine to run this on.
Yes, I understood that QIIME2 performs quality filtering step. So you think filtering would not help with the memory problem? Unfortunately I do not have access to a more powerful computer.
Should I change the settings for the virtual machine while running DADA2?
Any ideas how I could solve the problem without a more powerful computer?
Yes, give your virtual machine more memory if you can. Wow, 2048 MB is not much… you will probably need at least 4 GB RAM for an average dada2 run (that is a very rough guess). Let us know if that helps!