# Help in pre.cluster

**URL:** <https://forum.mothur.org/t/help-in-pre-cluster/21901>\
**Category:** Commands in mothur\
**Created:** [August 8, 2023, 1:27pm UTC](https://forum.mothur.org/t/help-in-pre-cluster/21901 "2023-08-08T13:27:13Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![allan\_santos](https://avatars.discourse-cdn.com/v4/letter/a/e19adc/32.png) [@allan\_santos](https://forum.mothur.org/u/allan_santos)\
**Post date:** [August 8, 2023, 1:27pm UTC](https://forum.mothur.org/t/help-in-pre-cluster/21901/1 "2023-08-08T13:27:13Z")

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Dear,  
after doing the alignment, screen.seqs, filter and unique, using fasta and count in most of them, I’ve done the pre.cluster with the following message.

**mothur \> pre.cluster(fasta=alr1.trim.unique.good.filter.unique.fasta, count=alr1.trim.unique.good.filter.count\_table, diffs=2)**  
**Using 64 processors.**  
**When using running without group information mothur can only use 1 processor, continuing.**  
**247654 97741 149913**  
**Total number of sequences before precluster was 247654.**  
**pre.cluster removed 149913 sequences.**

**/** \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\ ***/**  
**[WARNING]: alr1.trim.unique.good.filter.unique.fasta does not contain any sequence from the .accnos file.**  
**Selected 0 sequences from alr1.trim.unique.good.filter.unique.fasta.**

**Output File Names:**  
**alr1.trim.unique.good.filter.unique.precluster.fasta**

**/** \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\ ***/**  
**Done.**  
**It took 271 secs to cluster 247654 sequences.**

**Using 64 processors.**

\*\*Output File Names: \*\*  
**alr1.trim.unique.good.filter.unique.precluster.fasta**  
**alr1.trim.unique.good.filter.unique.precluster.count\_table**  
**alr1.trim.unique.good.filter.unique.precluster.map**

However, the outputted .precluster.fasta is empty and I cannot run chimera and the next steps.  
How can I solve that?  
thanks

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<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:** [August 8, 2023, 7:41pm UTC](https://forum.mothur.org/t/help-in-pre-cluster/21901/2 "2023-08-08T19:41:37Z")

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Hi Allan,

It looks like something, possibly related to your problem, happened upstream of this command. It doesn’t look like mothur has any of your group information. Can you make sure that you used a count\_table file with the earlier screen.seqs and unique.seqs (x2) commands?

Pat

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**Author:** ![allan\_santos](https://avatars.discourse-cdn.com/v4/letter/a/e19adc/32.png) [@allan\_santos](https://forum.mothur.org/u/allan_santos)\
**Post date:** [August 8, 2023, 8:18pm UTC](https://forum.mothur.org/t/help-in-pre-cluster/21901/3 "2023-08-08T20:18:44Z")

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Hi Pat,  
yes, I created again my group and count files in the previous steps and this problem was solved.  
thank you so much!!

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**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:** [August 18, 2023, 8:19pm UTC](https://forum.mothur.org/t/help-in-pre-cluster/21901/4 "2023-08-18T20:19:28Z")

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