# Chimera.vsearch does not update count table

**URL:** <https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407>\
**Category:** Uncategorized\
**Created:** [February 27, 2026, 2:16am UTC](https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407 "2026-02-27T02:16:44Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![JHC](https://avatars.discourse-cdn.com/v4/letter/j/e79b87/32.png) [@JHC](https://forum.mothur.org/u/JHC)\
**Post date:** [February 27, 2026, 2:16am UTC](https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407/1 "2026-02-27T02:16:44Z")

</div>

Hello:

I am following the MiSeq SOP using mothur v.1.48.5 (pre-compiled). Everything is going well until I get to the `chimera.vsearch` step. It appears that the `remove.seqs` command is not updating the count table that I provided. The relevant segment of the logfile is provided below.

I think I could work around this using the `removechimeras` option, followed by remove.seqs:

```auto
chimera.vsearch(fasta=current, count=current, dereplicate=t, removechimeras=f)
remove.seqs(fasta=current, count=current, accnos=current)

```

I just wanted to check in to see if I am calling `chimera.vsearch` incorrectly.

Thank you,

Jim

mothur \> chimera.vsearch(fasta=current, count=current, dereplicate=t)  
Using bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.count\_table as input file for the count parameter.  
Using bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.

Using 28 processors.  
Using vsearch version v2.16.0.  
Checking sequences from bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta …  
When using template=self, mothur can only use 1 processor, continuing.

It took 269 secs to check your sequences. 162586 chimeras were found.

Removing chimeras from your input files:  
/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/  
Running command: remove.seqs(fasta=bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta, accnos=bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos)  
Removed 162586 sequences from bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta.

Output File Names:  
bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.pick.fasta

/\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*/

Output File Names:  
bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras  
bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos  
bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta

mothur \> summary.seqs(fasta=current, count=current)  
Using bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.count\_table as input file for the count parameter.  
Using bc\_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta as input file for the fasta parameter.

Using 28 processors.  
[ERROR]: Your count file contains 187867 unique sequences, but your fasta file contains 25281. File mismatch detected, quitting command.

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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:** [March 5, 2026, 3:35pm UTC](https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407/2 "2026-03-05T15:35:37Z")

</div>

Does your dataset include samples? The line below indicates you are running the denovo method on a single sample. In that case, dereplicate is unnecessary.

> [@JHC](#):
>
> When using template=self, mothur can only use 1 processor, continuing.

Can you try running this command?

mothur \> chimera.vsearch(fasta=current, count=current)

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<div class="post-metadata">

**Author:** ![JHC](https://avatars.discourse-cdn.com/v4/letter/j/e79b87/32.png) [@JHC](https://forum.mothur.org/u/JHC)\
**Post date:** [March 5, 2026, 9:44pm UTC](https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407/4 "2026-03-05T21:44:05Z")

</div>

Thank you for the help.

I have 28 samples.

Jim

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<div class="post-metadata">

**Author:** ![JHC](https://avatars.discourse-cdn.com/v4/letter/j/e79b87/32.png) [@JHC](https://forum.mothur.org/u/JHC)\
**Post date:** [March 8, 2026, 7:31pm UTC](https://forum.mothur.org/t/chimera-vsearch-does-not-update-count-table/22407/5 "2026-03-08T19:31:52Z")

</div>

Your suggestion worked perfectly. Thank you for your help!

Jim