I’m switching to demultiplexing on the MiSeq and am trying to run make.contigs. It seems like it’s working till it hangs, though I do get an error after “processing file pair…” [Error]: Could not open 21021.num.temp (this error occurs 13 times which is the number of samples I’m trying to proccess). After the errors it starts make.contigs. I get “It took X seconds to assemble X reads” 13 times so again seems like it’s worked but after that it hangs for hours. I’ll upload the logfile