Hello there.
This is a continuation of the topic posted at:
As it has been closed due to inactivity.
I have a problem when trying to cluster eukaryotic sequences using either cluster or cluster.split.
After several tries where the system collapsed I ran dist.seqs with the column output option and then tried to run cluster.split like this:
cluster.split(column=Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist, count=Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, cutoff=0.03, large=T)
It is, with all the requierments to avoid the use of too much memory.
However, I got something like this:
Using 16 processors.
Splitting the file...
It took 529530 seconds to split the distance file.
Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.33.temp
Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.209.temp
Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.115.temp
Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.451.temp
Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.39.temp
(...)
Clustering Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.807.temp
Clustering Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.658.temp
Clustering Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.724.temp
Clustering Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.1118.temp
Clustering Eukarya_rocas.trim.contigs.good.unique.good.filter.unique.precluster.pick.dist.1293.temp
(...)
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
0 1428050402 0 1 0 1428050402 0 1 0 1428050402 0 1 0
1428050402 0 1 0 1428050402 0 1
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
(...)
And then, the process stops.
Any idea of what is happening? Could it be a problem of disk space? I am running mothur on a windows server with 16 processors and 64gb of RAM
Thanks