Problem with cluster.split and opti_mcc.list files


I was having trouble with the dist.seq command taking a long time to work and crashing at some point in the middle due to a network error, so I tried using the cluster.split command and found it sped things up immensely.

I now have a 165 GB final.dist file and 170 final.opti_mcc.list files.

To move on to the next step of my analysis, I need to perform the make.shared command, list=final.opti_mcc.list, but I don’t have a single file, instead I have around 170 final.opti_mcc.lists.

Not sure what to do from here. Would appreciate any help.

Edit: I need to mention that I skipped all of these steps:

mothur > dist.seqs(fasta=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.fasta, cutoff=0.03)
mothur > cluster(column=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.dist, count=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table)
mothur > make.shared(list=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.opti_mcc.list, count=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, label=0.03)
mothur > rarefaction.single(shared=stability.trim.contigs.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.opti_mcc.shared)

Because I couldn’t complete the first step (dist.seq) so I went to straight to the OTU section and did the cluster.split command.

You should delete all of those list files and run cluster.split again so you can start with a blank slate. That will make it easier to see what’s going on.

Also, if you are running this on a cluster you should try using tmux or screen so you don’t lose the work if you have to log out or get disconnected.