# cluster command

**URL:** <https://forum.mothur.org/t/cluster-command/3141>\
**Category:** Commands in mothur\
**Created:** [February 28, 2017, 3:20pm UTC](https://forum.mothur.org/t/cluster-command/3141 "2017-02-28T15:20:50Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![heyheyhey](https://avatars.discourse-cdn.com/v4/letter/h/da6949/32.png) [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\
**Post date:** [February 28, 2017, 3:20pm UTC](https://forum.mothur.org/t/cluster-command/3141/1 "2017-02-28T15:20:50Z")

</div>

Hi,

I’m using the MiSEQ SOP as a reference. I’m also in script mode. [https://www.mothur.org/wiki/MiSeq\_SOP](https://www.mothur.org/wiki/MiSeq_SOP)

The dist.seq and count.seqs commands works, but cluster quits. The code is below.

```nohighlight
`$mothur \"#dist.seqs(fasta=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta, cutoff=0.20, processors=$number_of_processors)\"`; 

`$mothur \"#count.seqs(name=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.names)\"`;

`$mothur \"#cluster(column=/home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.count_table)\"`;

```

The cluster command doesn’t spit out an output file. It runs for a while and then stops. Here’s the log file.

```nohighlight
[mpiuser@cluster ~]$ tail -50 mothur.1488203392.logfile
Linux version

Using ReadLine

Running 64Bit Version

mothur v.1.35.1
Last updated: 03/31/2015

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program
Script Mode

```

I also tried using cluster.split, but I’m getting errors.

```nohighlight
`$mothur \"#cluster.split(fasta=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta, count=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.count_table, taxonomy=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v123.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.02, processors=$number_of_processors)\"`;

```

```nohighlight
Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.1.dist
********************#**** # ****#**** # ****#**** # ****#**** # ****#**** # **** #
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.12.dist
Cutoff was 0.025 changed cutoff to 0.02
********************#**** # ****#**** # ****#**** # ****#**** # ****#**** # **** #
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.3.dist
Cutoff was 0.025 changed cutoff to 0.02
Cutoff was 0.025 changed cutoff to 0.02
[ERROR]: Could not open 31950.temp

```

I would like to get something clustered with either command. Does anyone have any ideas how I could improve this?

Thanks!

---

<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:** [February 28, 2017, 7:52pm UTC](https://forum.mothur.org/t/cluster-command/3141/2 "2017-02-28T19:52:10Z")

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Can you try our latest version, 1.39.3 [https://github.com/mothur/mothur/releases/tag/v.1.39.3](https://github.com/mothur/mothur/releases/tag/v.1.39.3)? It includes our new clustering method opti. The opti method uses significantly less time and memory, and produces better quality OTU assignments.

---

<div class="post-metadata">

**Author:** ![heyheyhey](https://avatars.discourse-cdn.com/v4/letter/h/da6949/32.png) [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\
**Post date:** [February 28, 2017, 8:06pm UTC](https://forum.mothur.org/t/cluster-command/3141/3 "2017-02-28T20:06:08Z")

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Will the latest cluster command work with 1.35 generated input?

---

<div class="post-metadata">

**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:** [March 2, 2017, 12:29pm UTC](https://forum.mothur.org/t/cluster-command/3141/4 "2017-03-02T12:29:51Z")

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It should. Everything should be backwards compatible.

Pat