Problem of Clearcut

Commands in mothur
1

Hello, I am trying to use the Clearcut command.
As the tutorial said, I run the dist.seqs comand first, generating the phylip formatted dist matrix.



mothur > dist.seqs(fasta=XXX.unique.fasta,cutoff=0.03,processors=2,output=lt); mothur > clearcut(phylip=XXX.unique.phylip.dist)

And the error is as follows:
Clearcut: Syntax error in distance matrix at offset 15.

I do not know much about clearcut, what I can do with this error?

2

I’m guessing the problem is that you’ve exceeded your virtual memory size. That can happen with big datasets.

3

Is the problem in this case actually because the dist.seqs output format is “lt” for the lower triangle matrix? Does clearcut require a square matrix input?

4

lt is fine. How big is the distance matrix?