# clearcut

**URL:** https://forum.mothur.org/t/clearcut/2896
**Category:** Commands in mothur
**Created:** [June 22, 2016, 7:15pm UTC](https://forum.mothur.org/t/clearcut/2896 "2016-06-22T19:15:37Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![slaperriere](https://avatars.discourse-cdn.com/v4/letter/s/67e7ee/32.png) [@slaperriere](https://forum.mothur.org/u/slaperriere)
#### Post date: [June 22, 2016, 7:15pm UTC](https://forum.mothur.org/t/clearcut/2896/1 "2016-06-22T19:15:37Z")

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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

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### Author: ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [June 23, 2016, 11:09am UTC](https://forum.mothur.org/t/clearcut/2896/2 "2016-06-23T11:09:21Z")

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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/](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