I'm trying to use the uparse_ref (http://www.drive5.com/usearch/manual/cmd_uparse_ref.html) command to annotate a set of reads from a MiSeq run. The database was generated by someone in my lab, and has worked in the past.

The issue I'm running into is that whenever I run the command, it hangs on the classifying step almost immediately after running, i.e. my terminal output freezes at

00:00 4.8Mb    0.1% Classifying

and I can't seem to do anything to overcome this. I've actually run a lab mate's pipeline (for whom the command worked) on my machine using all of their data, and the program still froze! Any ideas on how to move past this?