cluster.split(splitmethod=classify, taxlevel=3, cluster=f, method=opti, cutoff=0.05, column=final.dist, count=final.count_table, taxonomy=final.taxonomy) with mothur/1.44.3 on a Linux cluster, and I’m having 2 issues :
I want to redirect the temporary matrices created (e.g.
.dist.1.temp) in another existing directory with the use of
set.dir(output=/scratch/users/vgilbart, tempdefault=/scratch/users/vgilbart/temp), but this does not seem to work. It continues to create the
.dist.00.tempin the same folder as the original matrix (same thing for the
.count_table, although this is not my main issue). It only outputs the
.filein the directory I want.
Is there anyway I can change that or is it mandatory for the temp matrices to be written in the same folder as the original one?
I still carried on with the clustering by running
cluster.split(file=final.file, method=opti, cutoff=0.05)which had the following warning :
[WARNING]: Cannot run sens.spec analysis without a phylip or column file, skipping. Output File Names: final.opti_mcc.list
And then, I encountered an error while running
make.shared(list=final.opti_mcc.list, count=final.count_table) :
[ERROR]: SOME_SEQUENCE is in your groupfile and not your listfile. Please correct. Your group file contains 229716 sequences and list file contains 229712 sequences. Please correct.
I have seen this type of error happening to other in the forum, mostly due to mistakes in generating the
.group file before the clustering. But I have ran
make.shared() after another clustering method (agc and dgc, although I know the mothur team does not recommand these methods), with the same
.count_table file without any issue.
So I can only suppose the problem is due to sequences missing in the
.list file created by the
cluster.split() command? Or do you have another explanation as for why the
make.shared() command works with a
.list file created by
cluster(method=agc) but not by one created by the
cluster.split(method=opti, ...) command?
Thank you very much for your effort in documentation and this forum, it has already helped me a lot in better understanding mothur!