FAQs

Why does Unicycler take so long to finish?

Unicycler has never been especially fast, but there are a couple reasons it might be extra slow: too few threads or too many reads. See this issue thread for some tips on improving run times.

How can I compile Racon on a Mac?

I had issues with using Clang (the compiler that comes with Xcode) and instead had to use GCC. See this issue thread for how I got around the problem.

Why is Unicycler crashing in a virtual machine?

SPAdes seems to have some file system problems with its temporary directory in virtual machines. See issues 69 and 82 for more information.

Try using Unicycler's --spades_options to specify a location that's local in your virtual machine. For example:

unicycler -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o outdir --spades_options "--tmp-dir /tmp"