# NaN value after distmat in StrainPhlAn!

**URL:** <https://forum.biobakery.org/t/nan-value-after-distmat-in-strainphlan/5489>\
**Category:** StrainPhlAn\
**Created:** [June 19, 2023, 7:31am UTC](https://forum.biobakery.org/t/nan-value-after-distmat-in-strainphlan/5489 "2023-06-19T07:31:37Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Kim-Gihyeon](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kim-gihyeon/32/2182_2.png) [@Kim-Gihyeon](https://forum.biobakery.org/u/Kim-Gihyeon)\
**Post date:** [June 19, 2023, 7:31am UTC](https://forum.biobakery.org/t/nan-value-after-distmat-in-strainphlan/5489/1 "2023-06-19T07:31:37Z")

</div>

Hello developers,

I am running the StrainPhlAn referring latest _[tutorial](https://github.com/biobakery/biobakery/wiki/strainphlan4)_, and encountering some problems.  
I ran through the instructions and reached the step of producing an ordination plot.  
When I ran distmat by a code:

> `distmat -sequence strainphlan_output/t __SGB17248.StrainPhlAn4_concatenated.aln -nucmethod 2 -outfile strainphlan_output/t__ SGB17248.distmat`

I got a output file (~.distmat) whose one of samples had NaN value for all comparsion to other samples. This NaN made an error with running strainphlan\_ordination\_vis.R at \> `cmdscale()` function.

Some previous forums suggested turning NaN into 0, however, I doubt that it is correct.  
Do you have any suggestions or solutions?

Thank you  
Best regard, Gihyeon

_Tools [version]_

- distmat [EMBOSS:6.6.0.0]
- strainphlan [4.0.6]