# Clearcut truncates sequence names to 7 characters

**URL:** <https://forum.mothur.org/t/clearcut-truncates-sequence-names-to-7-characters/21313>\
**Category:** mothur bugs\
**Created:** [February 20, 2022, 11:15pm UTC](https://forum.mothur.org/t/clearcut-truncates-sequence-names-to-7-characters/21313 "2022-02-20T23:15:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![gwidmer](https://avatars.discourse-cdn.com/v4/letter/g/a8b319/32.png) [@gwidmer](https://forum.mothur.org/u/gwidmer)\
**Post date:** [February 20, 2022, 11:15pm UTC](https://forum.mothur.org/t/clearcut-truncates-sequence-names-to-7-characters/21313/1 "2022-02-20T23:15:53Z")

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I’m running mothur v. 47 on windows.  
Description of problem:

> clearcut(fasta=BacPop10.chop.unique.good.filter.unique.precluster.fasta, DNA=T, verbose=t)  
> unifrac.weighted(tree=BacPop10.chop.unique.good.filter.unique.precluster.tre, count=BacPop10.chop.unique.good.filter.unique.precluster.count\_table, distance=lt)

generates the following error:  
[ERROR]: M02058\_ is not in your count table. Please correct.  
[ERROR]: M06066\_ is not in your count table. Please correct.  
etc  
etc  
Here what the first few lines of the tree file generated by clearcut look like:  
((((((((((((((((((((((((((((((((((M06066\_:-0.000208,(M02058\_:-0.000202,(M06066\_:-0.000196,(M06066\_:-0.000191,(((((((((((((M06066\_:0.004497,(((((((M06066\_:0.000307,(M06066\_:0.000955,(((M06066\_:0.010741,M06066\_:0.016657):0.005434,(((((M06066\_:0.011 etc.

As indicated by the error message, the seqs names are truncated.

If I run clearcut on our galaxy instance, download the tree file and run unifrac.weighted in windows (v.47), unifrac runs fine. Here is what the first few lines of the tree file generated in galaxy look like:  
((((((M02058\_549\_000000000-BNC88\_1\_1101\_21424\_19684:0.004682,M06066\_61\_000000000-C4YPK\_1\_1102\_24380\_21149:0.004752):-0.000000,((((M02058\_520\_000000000-BKCRD\_1\_1111\_16117\_29088:0.004713,M06066\_91\_000000000-CCMK3\_1\_1104\_18642\_7041:0.004721):-0.000000,((M06066\_91\_000000000-CCMK3\_1\_2103\_16948\_13817:0.002374,M06066\_91\_000000000-

The seq names are complete. Galaxy runs mothur v. 39.5  
|Galaxy Tool ID:|toolshed.g2.bx.psu.edu/repos/iuc/mothur\_clearcut/mothur\_clearcut/1.39.5.0|  
|Galaxy Tool Version:|1.39.5.0|  
|Tool Version:|v.1.39.5|

Just to be sure, I replaced the hyphens in the seq names with underscores, which did not solve the problem.

thanks for your help,

Giovanni

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**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, 2022, 6:40pm UTC](https://forum.mothur.org/t/clearcut-truncates-sequence-names-to-7-characters/21313/2 "2022-02-28T18:40:17Z")

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Thanks for reporting this issue. I have fixed the bug and the change will be part of our next release. In the meantime try this:

mothur \> dist.seqs(fasta=BacPop10.chop.unique.good.filter.unique.precluster.fasta, output=lt)  
mothur \> clearcut(phylip=current)

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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:** [March 10, 2022, 6:40pm UTC](https://forum.mothur.org/t/clearcut-truncates-sequence-names-to-7-characters/21313/3 "2022-03-10T18:40:55Z")

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