I have some 16S MiSeq data that I am trying to run through the same pipeline as the MiSeq SOP. I have done this successfully until I get to the portion creating a tree. I’ve managed to use a high memory computer on the university cluster to overcome that hurdle, but Clearcut times out – potentially because it cannot run in parallel.
I recently started to try and use the ‘tree.shared’ function because it allows use of multiple CPUs. However despite having multiple processors available on the HPC cluster, I have not been able to make use of them using either the autodetect default or through explicitly specifying them with the ‘processors=’ argument.
Has anyone run into this issue? What types of workarounds have you used?
Thank you! This forum is wonderful.