# Remove.rare taking a long time to run

**URL:** https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826
**Category:** Commands in mothur
**Created:** [April 11, 2019, 5:39pm UTC](https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826 "2019-04-11T17:39:10Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![joelio1616](https://avatars.discourse-cdn.com/v4/letter/j/e5b9ba/32.png) [@joelio1616](https://forum.mothur.org/u/joelio1616)
#### Post date: [April 11, 2019, 5:39pm UTC](https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826/1 "2019-04-11T17:39:10Z")

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Hi,

I am trying to remove rare OTUs using the remove.rare command. Since I generated my list with a count table, I also included that in the command.

It has been running for about two days now. My list was based on unique sequences (not clustered based on 0.03), as I am working with data where SNPs are important for allele designation.

Is there any way to increase the speed of this process? I notice I cannot designate how many processors to use, and looking at the task manager it looks like it is only using one.

Any help is greatly appreciated.

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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: [April 17, 2019, 3:19pm UTC](https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826/2 "2019-04-17T15:19:53Z")

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Can you post the exact syntax you are using? ALso, what happens if you only provide the list file and not the count table?

Pat

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### Author: ![joelio1616](https://avatars.discourse-cdn.com/v4/letter/j/e5b9ba/32.png) [@joelio1616](https://forum.mothur.org/u/joelio1616)
#### Post date: [April 17, 2019, 5:22pm UTC](https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826/3 "2019-04-17T17:22:34Z")

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Hi Pat,

This has been resolved. I took your advice to contact [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) (via a twitter response).

The person helped immensely.

```
mothur > remove.rare(shared=mhc.shared, nseqs=2, label=0.0)
Your file does not include the label 0.0. I will use 0.
0

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.shared

mothur > list.otus(shared=current)
Using /Users/joel/Desktop/rare/mhc.0.pick.shared as input file for the shared parameter.
0

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.0.otulabels

mothur > get.otus(list=mhc.list, accnos=mhc.0.pick.0.otulabels)
You did not provide a label, I will use the first label in your inputfile.
Selected 95143 OTUs from your list file.

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.list

mothur > list.seqs(list=current)
Using /Users/joel/Desktop/rare/mhc.0.pick.list as input file for the list parameter.

Output File Names: 
/Users/joel/Desktop/rare/mhc.0.pick.accnos

mothur > get.seqs(count=mhc.count_table)
Using /Users/joel/Desktop/rare/mhc.0.pick.accnos as input file for the accnos parameter.
Selected 542001 sequences from your count file.

Output File Names: 
/Users/joel/Desktop/rare/mhc.pick.count_table
```

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<div class="post-metadata">

### Author: ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)
#### Post date: [April 27, 2019, 5:22pm UTC](https://forum.mothur.org/t/remove-rare-taking-a-long-time-to-run/19826/4 "2019-04-27T17:22:36Z")

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