QC-Chain is kind of messy to install, it is a pipeline composed of several tools developed by the same group, but they are not kept in sync. In addition, documentation is also a bit confusing, even though seems to pretty complete. In the end I gave up before using it, I may get back to it if someone says nice things about its results.
In the end, I decided to use either FastQ Screen (really easy to install, not so pretty graphics) or MGA (better output but not so simple to install and particularly run).
There is also BBDuk and SeqyClean, both of them may check for contamination using kmers, it may be more sensitive than FastQ Screen and MGA, which use Bowtie.