clearcut

Commands in mothur
1

Hello -

I am having a problem with clearcut (mothur v.1.37.6). I have run:

dist.seqs(fasta=stability.2015pairedends.trim.contigs.trim.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, output=lt, processors=8)

clearcut(phylip=stability.2015pairedends.trim.contigs.trim.good.unique.good.filter.unique.precluster.pick.pick.pick.phylip.dist)

I get the following error:
Clearcut: Memory allocation error in NJ_parse_distance_matrix()
Clearcut: Syntax error in distance matrix at offset 7.

Is it possible my distance matrix is too large? I have 812042 sequences.

Thank you!
Sarah

2

Correct, that is not likely to work. I suspect you have some data quality issues (see http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix/), but even still, I suspect that you would have too many unique sequences to generate a tree from MiSeq data.

Pat