Okay, it’s entirely possible this is intentional and not a bug. But it shut down one of my mothur runs and gave me fits trying to figure out what the problem was so here it is:
chimera.uchime is apparently set up to accept multiple fasta filenames following the fasta= tag, with each filename separated by a hyphen. This is similar to the make.groups command, for instance. However, in the unusual instance where a filename actually INCLUDES a hyphen, chimera.uchime blows up. Here’s the filename I tried to check that shut me down:
So, this isn’t exactly a bug – but it might be worth either removing the multiple file option or mentioning in the wiki that hyphens are a no-no.