I am running a large data set of V4-16S MiSeq Illumina samples.
The clustering step using opticlust ended up killed in the sens.spec() command.
I am not sure about the implications are or exactly where the process got stopped. Or if the list file generated is the same that would have been generated after the sens.spec() command finishes.
It sounds like a memory issue. The sens.spec command is memory intensive and not necessary to complete the clustering. You can skip this step by setting runsensspec=f, https://mothur.org/wiki/Cluster.split#runsensspec.
Thanks for your reply!
So I assume that the list (and dist) files that were created are the same that would be produce without running the senspec command? or should I run the clustering again?
Yes, you can use the list file created by cluster.split. The runsensspec option gives you the stats for the merged list file and does not effect the OTUs created. You can get those stats later by running the sens.spec with the list and dist file if you choose.