# problems with .names or .fasta files while using cluster

**URL:** <https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152>\
**Category:** Commands in mothur\
**Created:** [December 11, 2012, 12:04pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152 "2012-12-11T12:04:27Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![ma.fernandez](https://avatars.discourse-cdn.com/v4/letter/m/e79b87/32.png) [@ma.fernandez](https://forum.mothur.org/u/ma.fernandez)\
**Post date:** [December 11, 2012, 12:04pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152/1 "2012-12-11T12:04:27Z")

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I am triying to use cluster command after using split.abund and dist.seqs, with my .abund fasta and names files, but when I run it I get a message saying that many sequences are missing form one of them (.fasta or .names).

Am I using the wrong files?

Here is my commands sequence:

```nohighlight
split.abund(cutoff=1)
dist.seqs(fasta=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.fasta)
cluster(name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)
get.oturep()

```

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**Author:** ![Rene](https://avatars.discourse-cdn.com/v4/letter/r/7cd45c/32.png) [@Rene](https://forum.mothur.org/u/Rene)\
**Post date:** [December 11, 2012, 12:22pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152/2 "2012-12-11T12:22:03Z")

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Hi,

as far as I see it you are missing part of the necessary Cluster parameters, i.e. don´t provide the column- or phylip-formatted distance matrix. Have a look at the CLUSTER command in the wiki. Try the distance matrix you get from the dist.seqs command like this:  
cluster(column=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.dist, name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)

Good luck!

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [December 11, 2012, 12:30pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152/3 "2012-12-11T12:30:37Z")

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Did you give split.abund the right files? It looks like your fasta has a “pick” in it and the names file does not.

fasta=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.fasta  
name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names

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<div class="post-metadata">

**Author:** ![ma.fernandez](https://avatars.discourse-cdn.com/v4/letter/m/e79b87/32.png) [@ma.fernandez](https://forum.mothur.org/u/ma.fernandez)\
**Post date:** [December 11, 2012, 1:51pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152/4 "2012-12-11T13:51:22Z")

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Before this commands I have run a chimera.uchime and a remove.seqs. In this latter I haven’t removed seqs from the .names file, so I am trying to do that and see If it generates the .names file required to my cluster command

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<div class="post-metadata">

**Author:** ![ma.fernandez](https://avatars.discourse-cdn.com/v4/letter/m/e79b87/32.png) [@ma.fernandez](https://forum.mothur.org/u/ma.fernandez)\
**Post date:** [December 11, 2012, 3:47pm UTC](https://forum.mothur.org/t/problems-with-names-or-fasta-files-while-using-cluster/1152/5 "2012-12-11T15:47:06Z")

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I think that I have fixed the problem this way, you were right. It was a problem with the files.

Thanks a lot