A bit of an unorthodox question, but curious if there’s a work-around.
I am running cluster.split with commands identical to these (with my file names substituted).
cluster.split(fasta=final.fasta, name=final.names, taxonomy=final.taxonomy, taxlevel=4, cluster=f, processors=8)
I was able to generate the distance matrix (it’s huge, but I got it) and the Files file. However, I am running into RAM issues on the second cluster.split command. It generates about 75% of the .opti_mcc.list files before having issues. It seems that I can pass the Files file through multiple times with different samples included so I could potentially generate all the .opti.mcc.list files for all my samples. My question is how I could then generate the “stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.list” that you use as an input into make.shared. Is that possible? It seems like there is some command at the end of cluster.split that concatenates all the opti_mcc.list files for each sample into a grouped opti_mcc.list and I am trying to figure out how to do this once I have generated all the individual files through separate runs of the second cluster.split command.