Hello,
I’m running 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 ofset.dir(output=/scratch/users/vgilbart, tempdefault=/scratch/users/vgilbart/temp)
, but this does not seem to work. It continues to create the.dist.00.temp
in the same folder as the original matrix (same thing for the.count_table
, although this is not my main issue). It only outputs the.file
in 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 .count
or .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!
Best,
Valentine