I have tried to run the classify.rf command but Mothur just shuts down. I have looked at the log file but I dont get any errors.
The only thing I get is a line with “0.030” and then nothing.
I wonder if it has something to do with my design file which looks like this:
I dont have replicates which is why it looks like this.
The script Im trying to run is this:
cluster(phylip=muscle.pick.good.filter.pick.phylip.dist, cutoff=0.3, precision=1000)
sub.sample(list=muscle.pick.good.filter.pick.phylip.an.list, group=seqs.pick.good.pick.groups,name=muscle.pick.good.pick.names ,taxonomy=muscle.pick.good.filter.good.wang.pick.taxonomy, persample=T, size=47)
make.shared(list=muscle.pick.good.filter.pick.phylip.an.0.030.subsample.list, group=seqs.pick.good.pick.subsample.groups, label=0.030)
classify.otu(list=muscle.pick.good.filter.pick.phylip.an.0.030.subsample.list, group=seqs.pick.good.pick.subsample.groups, name=muscle.pick.good.pick.subsample.names ,taxonomy=muscle.pick.good.filter.good.wang.pick.subsample.taxonomy, label=0.03, cutoff=80, probs=F)
classify.rf(shared=muscle.pick.good.filter.pick.phylip.an.0.030.subsample.shared, design=design.design, numtrees=100)
I have also tried to use the “current” option throught to make sure I didnt make any typos but I run into the same problem anyway.