# summary.tax issue

**URL:** https://forum.mothur.org/t/summary-tax-issue/2118
**Category:** mothur bugs
**Created:** [November 7, 2014, 12:28pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118 "2014-11-07T12:28:24Z")
**Posts on this page:** 7
**Page:** 1

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### Author: ![martijm](https://avatars.discourse-cdn.com/v4/letter/m/97f17d/32.png) [@martijm](https://forum.mothur.org/u/martijm)
#### Post date: [November 7, 2014, 12:28pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/1 "2014-11-07T12:28:24Z")

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Hi. I am sorry: I opened an issue in your github repository, but I have seen that you probably prefer the forum to tackle with this staff. So, I paste here the link:

> <https://github.com/mothur/mothur/issues/8>
>
> Hi. I faced this issue using classify.seqs. It failed both with wang and knn methods (this latter even without .taxonomy file...

Many thanks,  
Jose

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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: [November 10, 2014, 7:11pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/2 "2014-11-10T19:11:41Z")

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Mothur is expecting WYSVI\_02345\_02960 to be in the first column of the name file indicating it is unique. Is this the case?

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### Author: ![martijm](https://avatars.discourse-cdn.com/v4/letter/m/97f17d/32.png) [@martijm](https://forum.mothur.org/u/martijm)
#### Post date: [November 25, 2014, 3:13pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/3 "2014-11-25T15:13:44Z")

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Thank you very much for your reply. I apologize for my delay, I was expecting a notification from the forum (sorry, I did not enable it…) or an answer through github.

Unexpectedly, the WYSVI\_02345\_02960 problematic label had disappeared from the name file, as you suspected. So, I changed the name and group files to a previous version (I mean ‘done before’ in terms of the pipeline [http://www.mothur.org/wiki/Ion\_Torrent\_sequence\_analysis\_using\_Mothur](http://www.mothur.org/wiki/Ion_Torrent_sequence_analysis_using_Mothur)). The problem remains, but with a different label that, in this case, it is indeed in the first column of the name file:

```nohighlight
mothur > summary.tax(taxonomy=run2.shhh.trim.unique.good.filter.nr_v119.wang.taxonomy, name=run2.shhh.names, group=run2.shhh.groups)

reftaxonomy is not required, but if given will keep the rankIDs in the summary file static.
[ERROR]: WYSVI_00540_01863 is not in your name file please correct.
$ egrep WYSVI_00540_01863 run2.shhh.names 
WYSVI_00540_01863 WYSVI_00540_01863

```

Thanks!

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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: [December 1, 2014, 9:08pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/4 "2014-12-01T21:08:30Z")

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Could you send your files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)?

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### Author: ![martijm](https://avatars.discourse-cdn.com/v4/letter/m/97f17d/32.png) [@martijm](https://forum.mothur.org/u/martijm)
#### Post date: [December 4, 2014, 5:56pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/5 "2014-12-04T17:56:56Z")

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Done!  
Thanks

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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: [December 4, 2014, 9:40pm UTC](https://forum.mothur.org/t/summary-tax-issue/2118/6 "2014-12-04T21:40:58Z")

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You have sequences in your taxonomy file with the same name. For example:

line 67484  
WYSVI\_00540\_01863 Bacteria(81);

line 60545  
WYSVI\_00540\_01863 Bacteria(83);

Mothur removes sequences it read in the names file from memory as it reads them in the taxonomy file to save time and space. Mothur expects sequence names to be unique. Did you modify these files outside of mothur?

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### Author: ![martijm](https://avatars.discourse-cdn.com/v4/letter/m/97f17d/32.png) [@martijm](https://forum.mothur.org/u/martijm)
#### Post date: [December 5, 2014, 11:10am UTC](https://forum.mothur.org/t/summary-tax-issue/2118/7 "2014-12-05T11:10:03Z")

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Thank you very much for your help.

No, I did not modify the files outside of mothur. I used MPI against 64 cores, could it be a trouble of wrong data-chunk distribution among cores?
