chimera.uchime running for ever

Hey guys!

I am new to Microbiome analysis and Mothur. I was running the chimera.uchime code for my 96 samples (3,529,000 unique sequences) but the chimera.uchime has been running for almost 2 days. Does it usually take this long? All my previous steps took only 4-5 hours max.
Please reply :slight_smile:

You have other problems if you have 3.5 million unique sequences. Are you using the MiSeq SOP? Can you post hte commands you are running?