I'm running Unicycler in virtualbox (because I can't get racon to compile on macosx), and SPAdes doesn't like that I've mounted my working directory using vboxfs (something about a bug in mmap). The SPAdes folks suggested I use '--tmp-dir' and point it to a virtualbox-local site like /tmp, and that works.

To get Unicycler to work in the vbox, I hacked spades_func.py to include '--tmp-dir /tmp' in the 'command' for SPAdes and it worked. You might want to include something like this, or an option to pass-through arguments to SPAdes.

thanks!